Contacts of the helix formed by residues 116 - 131 (chain A) in PDB entry 5A5J
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 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 4.4 0.2 - - - +
96A GLY* 3.5 8.4 - - - -
97A ARG* 3.0 46.0 + - - +
109A GLY 5.0 0.8 + - - -
114A PHE 4.8 4.4 + - - -
115A SER* 1.3 81.2 + - - +
117A GLY* 1.3 70.9 + - - +
118A LYS 2.8 4.7 + - - -
119A LYS* 3.5 13.1 + - - +
120A TRP* 3.4 15.5 + - - +
433A ARG* 3.3 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 1.3 75.8 + - - +
118A LYS* 1.3 57.6 + - - -
120A TRP* 3.9 9.1 - - - +
121A LYS* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN 2.8 4.9 + - - -
117A GLY* 1.3 71.0 - - - -
119A LYS* 1.3 64.4 + - - +
120A TRP 3.2 0.9 - - - -
121A LYS* 3.6 11.2 - - + +
122A GLU* 3.2 48.8 + - - +
279A PRO 5.3 6.3 + - - -
280A SER* 6.1 0.2 - - - +
281A GLU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY 4.0 11.8 + - - -
110A PHE* 2.9 52.4 - - + -
115A SER* 4.6 9.4 - - - -
116A ASN 3.5 11.2 + - - +
118A LYS* 1.3 76.1 - - - +
120A TRP* 1.3 62.9 + - - +
122A GLU* 4.1 0.3 - - - +
123A ILE* 3.1 42.0 + - + +
281A GLU* 2.8 40.1 + - + +
286A SER* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 3.4 26.7 - - - -
112A ILE* 3.3 28.7 - - + -
115A SER* 3.6 12.9 + - - +
116A ASN* 3.4 22.0 + - - +
117A GLY 4.2 8.1 - - - -
119A LYS* 1.3 79.1 - - - +
121A LYS* 1.3 87.6 + - + +
122A GLU 3.1 1.0 + - - -
123A ILE* 4.8 2.0 - - - -
124A ARG* 3.1 45.3 + - + +
432A LYS* 3.2 38.1 - - + -
433A ARG* 3.2 37.7 - - - -
1493A HEM 2.8 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.3 24.8 + - - +
117A GLY 3.3 16.7 + - - +
118A LYS* 3.3 12.5 + - + +
120A TRP* 1.3 95.4 - - + +
122A GLU* 1.3 63.8 + - + +
124A ARG* 4.2 1.4 - - - +
125A ARG* 3.4 25.9 + - + +
432A LYS* 5.0 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.2 32.3 + - - +
119A LYS 4.2 1.6 - - - +
121A LYS* 1.3 82.3 - - + +
123A ILE* 1.3 62.0 + - - +
125A ARG* 3.7 5.6 - - - +
126A PHE* 3.2 18.2 + - - +
274A GLU* 5.4 5.6 - - - +
280A SER* 5.4 0.3 + - - -
281A GLU* 3.1 32.8 + - + +
282A PHE* 3.4 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE 4.1 11.7 - - - +
111A GLY 4.1 6.5 - - - +
112A ILE* 4.0 16.2 - - + -
119A LYS* 3.1 28.4 + - + +
120A TRP* 4.2 0.7 - - - +
122A GLU* 1.3 81.1 - - + +
124A ARG* 1.3 60.5 + - - +
125A ARG 3.2 0.2 - - - -
126A PHE* 3.2 6.8 + - + +
127A SER* 2.8 40.3 + - - +
267A PHE* 5.4 5.6 - - + -
281A GLU* 4.0 21.1 - - + +
282A PHE* 4.4 15.0 - - + -
286A SER* 4.0 17.5 - - - +
290A THR* 3.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.9 17.2 - - + +
120A TRP* 3.1 48.5 + - + +
121A LYS* 4.2 2.2 - - - +
123A ILE* 1.3 80.2 - - - +
125A ARG* 1.3 54.1 + - - +
127A SER* 3.1 5.2 + - - -
128A LEU* 2.8 56.7 + - - +
432A LYS* 3.5 19.6 + - - +
434A ILE* 2.6 46.9 + - - +
436A VAL* 3.9 23.7 - - + +
1493A HEM 3.9 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 3.4 22.5 + - + +
122A GLU* 3.7 7.6 - - - +
123A ILE 3.2 0.4 - - - -
124A ARG* 1.3 76.9 - - - +
126A PHE* 1.3 68.0 + - - +
128A LEU* 3.3 15.1 - - - +
129A MET* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU 3.2 13.0 + - - +
123A ILE* 3.2 8.9 + - + +
125A ARG* 1.3 81.2 - - - +
127A SER* 1.3 60.9 + - - +
129A MET* 3.2 5.8 + - + +
130A THR* 2.4 45.3 + - + -
263A PHE* 4.3 10.5 - + - -
266A CYS* 3.4 26.0 - - - -
267A PHE* 3.4 55.0 - + + -
270A LYS* 3.7 37.2 - - + -
282A PHE* 3.8 14.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.9 18.4 - - - +
123A ILE* 2.8 21.9 + - - +
124A ARG* 3.7 3.1 - - - -
126A PHE* 1.3 75.1 - - - +
128A LEU* 1.3 56.9 + - - +
130A THR* 3.1 2.6 + - - -
131A LEU* 2.8 48.4 + - - +
263A PHE* 3.2 31.6 - - - -
290A THR* 3.8 13.5 - - - +
294A LEU* 5.6 0.9 - - - -
436A VAL* 4.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 2.8 44.9 + - - +
125A ARG* 3.3 17.9 - - - +
127A SER* 1.3 74.1 - - - +
129A MET* 1.3 78.9 + - - +
131A LEU* 3.2 17.1 + - - +
132A ARG* 3.3 30.1 - - + +
436A VAL* 4.0 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.0 31.4 - - + +
126A PHE* 3.2 6.8 + - + +
127A SER 3.2 0.8 - - - -
128A LEU* 1.3 100.5 - - - +
130A THR* 1.3 65.2 + - - +
131A LEU 3.2 0.4 - - - -
132A ARG* 3.3 7.9 + - + +
134A PHE* 3.0 72.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 2.4 38.5 + - + -
127A SER 3.4 5.2 - - - -
129A MET* 1.3 74.7 - - - +
131A LEU* 1.3 58.2 + - - +
132A ARG 2.9 9.3 + - - -
133A ASN 3.2 7.4 + - - -
134A PHE 4.1 6.7 + - - -
136A MET* 3.0 52.6 - - + +
263A PHE* 3.3 28.5 - - + -
266A CYS* 3.7 19.4 - - + -
----------------------------------------------------------
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 SER* 2.8 29.8 + - - +
128A LEU* 3.4 7.6 - - - +
129A MET 3.2 0.4 - - - -
130A THR* 1.3 78.1 - - - +
132A ARG* 1.3 63.8 + - + +
133A ASN 3.7 0.4 - - - -
141A ILE* 3.9 26.2 - - + +
181A ILE* 3.9 32.3 - - + -
263A PHE* 4.5 8.7 - - + -
294A LEU* 4.8 11.7 - - + -
436A VAL* 3.9 28.9 - - + +
437A GLY* 5.8 0.9 - - - -
439A ALA* 6.1 0.7 - - - +
440A LEU* 5.8 9.6 - - + +
1493A HEM 4.3 20.2 - - + -
----------------------------------------------------------
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