Contacts of the helix formed by residues 112 - 135 (chain A) in PDB entry 4PKO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY 3.7 2.3 + - - -
111A MET* 1.3 70.9 - - - +
113A PRO* 1.3 71.4 - - - +
114A MET* 3.2 16.3 + - - +
115A ASP* 2.9 44.7 + - + +
116A LEU* 3.0 28.0 + - - +
118A ARG* 4.7 2.4 - - - +
435A ASP* 3.4 12.5 + - - +
33B PRO 5.1 0.4 + - - -
34B LYS* 3.8 46.5 - - + +
36B ARG* 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 5.8 0.4 - - - +
107A VAL* 4.1 10.1 - - + -
111A MET 3.2 10.3 - - - +
112A ASN* 1.3 90.0 - - - +
114A MET* 1.3 64.1 + - - +
116A LEU* 3.0 23.7 + - + +
117A LYS* 3.1 14.0 + - - +
515A ILE* 3.3 27.9 - - + +
516A THR* 3.9 16.0 - - - +
36B ARG* 3.6 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.2 14.0 + - - +
113A PRO* 1.3 78.7 - - - +
115A ASP* 1.3 59.5 + - - +
117A LYS* 3.8 14.6 + - + +
118A ARG* 3.3 57.9 + - + +
516A THR* 4.5 18.1 - - - +
33B PRO 4.0 13.9 - - - +
34B LYS* 5.2 0.2 - - - -
35B GLY 4.6 15.0 - - - +
36B ARG* 6.1 0.6 - - - +
37B ASN* 4.7 11.2 - - - +
51B LYS* 5.4 4.3 - - + -
153B ASN* 3.2 25.8 - - - +
391B GLU* 5.1 11.0 - - - +
395B ARG* 5.3 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 2.9 38.5 + - + +
113A PRO 3.1 0.2 - - - -
114A MET* 1.3 78.9 - - - +
116A LEU* 1.3 63.3 + - - +
117A LYS 3.3 0.2 - - - -
118A ARG* 3.5 13.3 + - - +
119A GLY* 3.1 17.3 + - - -
433A ASN* 3.4 25.6 + - - -
435A ASP* 4.0 12.6 - - + +
436A GLN* 3.2 35.1 + - + +
34B LYS* 4.7 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 3.9 11.9 - - - +
106A ALA* 3.6 27.1 - - + -
107A VAL* 4.3 13.0 - - + -
111A MET* 4.7 10.1 - - + +
112A ASN 3.0 17.7 + - - +
113A PRO* 3.0 9.8 + - + +
115A ASP* 1.3 73.4 - - - +
117A LYS* 1.3 59.6 + - - +
119A GLY* 3.3 1.7 + - - -
120A ILE* 3.0 36.8 + - + +
435A ASP* 3.4 24.9 - - - +
438A VAL* 4.2 13.5 - - + -
439A GLY* 3.7 18.6 - - - +
442A VAL* 5.3 2.9 - - + -
515A ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO 3.1 10.1 + - - +
114A MET* 3.9 20.0 - - + +
116A LEU* 1.3 74.9 - - - +
118A ARG* 1.3 66.1 - - + +
120A ILE* 3.3 8.6 + - - +
121A ASP* 2.9 58.5 + - - +
509A SER* 4.0 12.5 + - - +
512A GLY* 3.5 29.9 - - - +
513A LEU* 4.1 26.7 - - + +
515A ILE* 4.7 1.0 - - - +
516A THR* 4.6 8.1 - - + -
388B GLU* 3.3 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 4.7 2.4 - - - +
114A MET* 3.3 57.3 + - + +
115A ASP* 3.7 17.7 + - - +
116A LEU 3.3 0.2 - - - -
117A LYS* 1.3 82.1 - - + +
119A GLY* 1.3 62.2 + - - +
121A ASP* 3.8 6.1 + - - +
122A LYS* 3.5 20.8 + - - +
432A GLN* 5.5 2.0 - - - -
436A GLN* 4.1 23.1 - - - +
33B PRO* 4.7 7.7 + - - +
153B ASN* 4.0 24.9 + - - +
154B SER* 4.5 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP 3.1 13.7 + - - -
116A LEU 3.7 3.8 - - - -
117A LYS 3.1 0.2 - - - -
118A ARG* 1.3 76.2 - - - +
120A ILE* 1.3 64.3 + - - +
122A LYS* 3.4 4.8 + - - +
123A ALA 3.4 8.5 + - - -
436A GLN* 3.8 26.6 - - - +
439A GLY 3.8 6.7 - - - -
440A ILE* 3.2 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 4.0 27.6 - - + +
103A GLY* 6.0 0.2 - - - -
116A LEU* 3.0 17.3 + - + +
117A LYS* 3.3 6.9 + - - +
119A GLY* 1.3 74.2 - - - +
121A ASP* 1.3 67.5 + - - +
123A ALA* 3.0 6.1 + - - +
124A VAL* 2.9 32.2 + - + +
439A GLY* 3.1 23.3 + - - +
442A VAL* 4.7 9.9 - - + -
443A ALA* 3.9 19.7 - - + +
508A ALA* 4.4 15.7 - - + +
512A GLY* 4.7 7.4 - - - -
515A ILE* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 2.9 50.2 + - - +
118A ARG* 4.0 6.4 - - - +
120A ILE* 1.3 83.2 - - - +
122A LYS* 1.3 61.0 + - - +
124A VAL* 3.3 8.3 + - - +
125A THR* 2.9 30.4 + - - +
508A ALA* 4.6 14.4 - - - +
509A SER* 5.2 1.6 - - - -
512A GLY* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG 3.5 10.9 + - - +
119A GLY* 3.4 10.2 + - - +
120A ILE 3.2 0.6 - - - -
121A ASP* 1.3 75.3 - - - +
123A ALA* 1.3 67.0 + - - +
125A THR* 3.5 6.6 + - - -
126A ALA* 3.3 21.3 + - - +
429A LEU* 3.7 21.9 - - + +
430A ARG 2.8 28.1 + - - +
431A GLY* 4.3 10.4 - - - -
432A GLN* 6.2 1.2 - - - +
436A GLN* 6.1 0.4 - - - +
440A ILE* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 3.4 5.6 + - - +
120A ILE 3.0 9.3 + - - +
122A LYS* 1.3 77.3 - - - +
124A VAL* 1.3 58.3 + - - +
126A ALA 3.3 1.0 + - - -
127A ALA* 3.0 24.5 + - - +
426A LEU* 3.3 11.5 - - - +
429A LEU* 3.9 13.0 - - + +
440A ILE* 3.9 36.3 - - + +
443A ALA* 4.0 10.1 - - + -
444A LEU* 4.6 9.9 - - + -
447A MET* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 6.1 0.7 - - + -
120A ILE* 2.9 23.3 + - + +
121A ASP* 3.6 11.2 - - - +
123A ALA* 1.3 77.6 - - - +
125A THR* 1.3 55.0 + - - +
127A ALA* 3.0 9.2 + - - +
128A VAL* 2.7 43.5 + - + +
443A ALA* 5.1 5.6 - - + -
447A MET* 6.4 1.1 - - - -
504A LEU* 3.4 32.1 - - + -
505A GLN* 4.6 13.0 - - + -
508A ALA* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 2.9 18.1 + - - +
122A LYS* 3.8 7.0 - - - -
123A ALA 3.4 0.2 - - - -
124A VAL* 1.3 76.8 - - - +
126A ALA* 1.3 57.7 + - - +
128A VAL* 3.4 9.3 + - + +
129A GLU* 3.0 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 3.3 11.3 + - + +
123A ALA 3.5 8.1 - - - +
124A VAL 3.2 0.4 - - - -
125A THR* 1.3 78.6 - - - +
127A ALA* 1.3 51.2 + - - +
129A GLU* 3.1 11.9 + - - +
130A GLU* 2.8 35.3 + - - +
426A LEU* 3.5 26.0 - - + +
429A LEU* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 3.0 13.6 + - - +
124A VAL* 3.0 12.4 + - - +
126A ALA* 1.3 73.1 - - - +
128A VAL* 1.3 54.8 + - - +
130A GLU* 3.0 9.7 + - - +
131A LEU* 2.7 40.2 + - + +
422A VAL* 3.8 5.0 - - + +
426A LEU* 3.3 14.5 - - + +
447A MET* 3.8 29.4 - - + -
504A LEU* 5.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 2.7 31.5 + - + +
125A THR* 3.6 9.6 - - + +
127A ALA* 1.3 69.5 - - - +
129A GLU* 1.3 71.9 + - - +
131A LEU* 3.2 10.3 + - + +
132A LYS* 3.0 40.9 + - + +
501A ARG* 4.0 18.2 - - + +
504A LEU* 5.1 4.5 - - + -
505A GLN* 3.6 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 3.0 28.6 + - + +
126A ALA* 3.1 11.9 - - - +
128A VAL* 1.3 82.2 - - - +
130A GLU* 1.3 63.6 + - + +
132A LYS* 3.6 10.5 + - - +
133A ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 2.8 16.3 + - - +
127A ALA* 3.0 11.9 + - - +
129A GLU* 1.3 79.4 - - + +
131A LEU* 1.3 54.7 + - - +
133A ALA* 3.4 8.3 + - - +
134A LEU* 3.0 31.5 + - - +
422A VAL* 3.7 25.5 - - + +
425A LYS* 3.3 42.0 + - - +
426A LEU* 4.1 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 2.7 22.6 + - + +
128A VAL* 3.2 9.6 + - + +
130A GLU* 1.3 70.5 - - - +
132A LYS* 1.3 61.3 + - - +
133A ALA 3.1 1.3 - - - -
134A LEU* 3.3 5.3 + - + +
135A SER* 2.8 29.8 + - - -
412A VAL* 4.2 12.2 - - + +
418A ALA* 4.2 21.5 - - + +
419A LEU* 4.5 8.1 - - + -
422A VAL* 3.6 23.1 - - + -
497A THR* 3.9 12.9 - - + +
500A THR* 3.6 28.0 - - + +
501A ARG* 3.7 27.8 - - + +
504A LEU* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.0 35.6 + - + +
129A GLU* 4.2 10.1 - - - +
131A LEU* 1.3 76.7 - - + +
133A ALA* 1.3 60.8 + - - +
135A SER* 3.5 19.9 - - - +
409A GLU* 2.9 37.7 + - + +
497A THR* 4.9 3.4 - - + -
501A ARG* 4.2 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU 3.1 17.7 + - - +
130A GLU* 3.6 12.1 - - - +
131A LEU 3.1 0.8 - - - -
132A LYS* 1.3 76.3 - - - +
134A LEU* 1.3 61.0 - - - +
135A SER 3.1 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.0 19.9 + - - +
131A LEU* 4.0 4.7 - - + +
133A ALA* 1.3 74.1 - - - +
135A SER* 1.3 64.4 - - - +
136A VAL* 3.2 14.9 + - + +
411A VAL 4.3 0.2 - - - +
412A VAL* 3.5 33.2 - - + -
413A ALA* 4.6 5.8 - - + +
418A ALA* 5.5 5.8 - - + +
421A ARG* 4.6 24.5 - - + -
422A VAL* 5.2 8.7 - - + -
425A LYS* 6.2 3.4 - - - +
474A GLY* 6.5 0.7 - - - -
475A ASN* 5.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 2.8 16.9 + - - -
132A LYS* 3.5 15.5 - - - +
133A ALA 3.1 7.3 - - - +
134A LEU* 1.3 77.1 - - - +
136A VAL* 1.3 61.7 + - - +
137A PRO* 4.4 3.5 - - - +
409A GLU* 2.8 25.7 + - - -
410A GLY* 3.7 3.6 - - - -
411A VAL 3.9 6.1 - - - -
412A VAL* 4.1 0.9 - - - -
497A THR* 3.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il