Contacts of the helix formed by residues 119 - 137 (chain A) in PDB entry 4XZC
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 GLU 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL 5.1 3.6 - - - -
118A PRO* 1.3 77.3 - - - +
120A PRO* 1.3 75.5 - - + +
121A GLU* 3.2 27.8 - - - +
122A GLN* 3.0 32.9 + - - +
123A LEU* 3.5 7.1 + - - +
226A ARG* 3.2 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO 4.0 1.8 - - - +
119A GLU* 1.3 90.0 - - + +
121A GLU* 1.3 60.5 + - - +
123A LEU* 3.0 16.9 + - + +
124A VAL* 2.9 30.6 + - - +
226A ARG* 4.4 8.7 - - - +
237A VAL* 4.9 6.1 - - + -
241A GLU* 4.5 8.7 - - - +
291A LEU* 3.8 29.2 - - + +
294A LYS* 4.7 3.7 - - + +
295A SER* 3.1 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 18.2 - - + +
119A GLU* 3.3 17.6 - - - +
120A PRO* 1.3 77.1 - - - +
122A GLN* 1.3 59.6 + - + +
124A VAL* 3.7 10.9 - - + +
125A ALA* 2.8 29.8 + - - +
226A ARG* 2.9 39.6 + - - -
227A SER* 2.7 36.2 + - - +
229A ILE* 4.7 14.5 - - + +
291A LEU* 4.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 2.9 40.4 + - + +
106A TRP* 3.7 5.2 - - + +
109A LYS* 3.6 21.8 - - - +
112A ASP* 5.3 2.2 + - - -
113A LEU* 3.6 20.0 - - - +
118A PRO* 3.5 11.3 - - + +
119A GLU* 3.0 39.0 + - - +
121A GLU* 1.3 83.4 - - + +
123A LEU* 1.3 57.4 + - - +
125A ALA* 3.7 6.6 - - - +
126A TYR* 3.1 18.9 + - - +
377A HIS* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 3.5 13.7 - - + +
119A GLU 3.9 11.7 - - - +
120A PRO* 3.0 14.3 + - + +
122A GLN* 1.3 75.0 - - - +
124A VAL* 1.3 64.8 + - - +
126A TYR* 3.3 3.3 + - - +
127A GLN* 3.0 33.0 + - + +
294A LYS* 4.4 17.7 - - + +
295A SER* 5.6 1.3 - - - +
298A LEU* 3.6 46.2 - - + -
303A ALA* 6.0 0.2 - - - -
377A HIS* 3.3 26.5 - - + -
378A PRO* 3.8 16.8 - - + -
471A TYR* 6.5 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
120A PRO 2.9 22.7 + - - +
121A GLU* 3.7 9.4 - - - +
123A LEU* 1.3 76.7 - - - +
125A ALA* 1.3 62.6 + - - +
127A GLN* 3.6 1.4 + - - +
128A ARG* 3.2 61.7 + - - +
290A GLU* 4.7 9.4 - - + +
291A LEU* 4.2 15.0 - - + -
294A LYS* 3.6 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.2 10.6 - - - +
105A LEU* 4.0 20.0 - - + -
106A TRP* 3.8 16.8 - - + +
121A GLU 2.8 18.6 + - - +
122A GLN 3.7 5.4 - - - +
123A LEU 3.2 0.2 - - - -
124A VAL* 1.3 78.6 - - - +
126A TYR* 1.3 57.0 + - - +
128A ARG* 3.8 9.4 - - - +
129A ALA* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 3.5 23.7 - + - +
122A GLN 3.1 17.8 + - - +
123A LEU* 3.3 4.5 + - - +
125A ALA* 1.3 76.5 - - - +
127A GLN* 1.3 86.5 + - + +
129A ALA* 3.4 3.3 + - - +
130A ALA* 3.0 26.7 + - + +
304A GLN 3.8 4.3 - - - -
306A ASP* 3.1 30.6 + - + +
309A PHE* 3.5 26.3 - + - -
310A SER* 2.6 30.2 + - - -
377A HIS* 3.6 23.8 - + + +
378A PRO* 3.5 27.5 + - + -
379A GLY* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.0 19.7 + - + +
124A VAL* 4.2 4.5 - - - +
126A TYR* 1.3 95.0 - - - +
128A ARG* 1.3 64.5 + - + +
130A ALA* 3.7 5.2 + - - +
131A GLN* 3.4 24.4 + - - +
294A LYS* 5.5 2.5 - - - -
304A GLN* 3.2 28.6 + - - +
306A ASP* 5.4 1.8 - - - +
378A PRO* 4.5 3.2 - - - +
469A ASN* 4.1 13.9 + - - -
471A TYR* 3.3 57.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 5.2 0.9 - - - -
124A VAL* 3.2 44.7 + - + +
125A ALA* 4.0 7.2 - - - +
127A GLN* 1.3 78.3 - - + +
129A ALA* 1.3 65.5 + - - +
131A GLN* 3.1 8.7 + - + +
132A LYS* 2.9 23.5 + - - +
290A GLU* 5.4 6.2 + - - +
294A LYS* 6.0 2.9 - - - +
472A LYS* 6.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TRP* 3.7 4.5 - - + -
102A VAL* 3.8 33.3 - - + +
103A ILE* 4.3 3.6 - - + -
106A TRP* 4.1 10.1 - - + -
125A ALA 2.8 18.2 + - - +
126A TYR 3.5 5.8 - - - +
128A ARG* 1.3 76.0 - - - +
130A ALA* 1.3 57.0 + - - +
132A LYS* 3.1 5.2 + - - +
133A TRP* 2.9 28.1 + - - +
309A PHE* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.0 18.1 + - + +
127A GLN* 3.7 9.6 - - - +
129A ALA* 1.3 74.4 - - - +
131A GLN* 1.3 62.9 + - - +
133A TRP* 3.4 2.4 - - - +
134A ARG* 3.1 29.9 + - - +
306A ASP* 3.6 26.2 - - + +
309A PHE* 3.7 29.3 - - + -
469A ASN* 4.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN 3.4 12.7 + - - +
128A ARG* 3.1 13.2 + - - +
130A ALA* 1.3 76.4 - - - +
132A LYS* 1.3 67.2 + - - +
134A ARG* 3.1 10.5 + - - +
135A GLN* 3.0 47.7 + - - +
140A GLU* 4.3 3.6 - - - +
147A SER* 2.4 37.3 + - - -
469A ASN* 3.4 23.8 + - - +
472A LYS* 4.5 20.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
95A TRP* 4.0 2.9 - - + -
99A ASN* 2.8 26.4 + - - +
102A VAL* 3.8 26.0 - - + -
128A ARG 2.9 12.4 + - - +
129A ALA* 3.4 9.4 - - - +
131A GLN* 1.3 77.1 - - - +
133A TRP* 1.3 53.7 + - - +
135A GLN* 3.0 10.2 + - - +
136A ASP* 2.6 73.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.3 12.6 - - - -
92A GLY* 3.1 36.6 + - - -
95A TRP* 3.3 38.6 - + + +
96A PHE* 3.7 3.8 - + - -
129A ALA 2.9 8.3 + - - +
130A ALA 3.4 9.2 - - - +
132A LYS* 1.3 74.7 - - - +
134A ARG* 1.3 68.5 + - + +
137A ASN* 2.8 59.4 + - + +
139A PHE* 4.0 25.1 - + + -
308A ILE* 3.8 21.8 - - + -
309A PHE* 3.5 33.4 - + + -
312A TYR* 3.5 36.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA 3.1 15.5 + - - +
131A GLN* 3.1 14.6 + - - +
133A TRP* 1.3 86.3 - - + +
135A GLN* 1.3 60.8 + - + +
138A LYS* 3.4 2.6 + - - -
139A PHE* 3.0 45.7 + - + -
140A GLU* 3.2 35.8 + - + +
145A THR 2.8 29.5 + - - -
146A ARG 4.2 0.4 - - - -
147A SER* 3.9 6.7 - - - -
306A ASP* 2.9 38.1 + - - +
308A ILE* 3.8 11.8 - - - +
309A PHE* 5.8 0.4 - - + -
466A HIS 5.1 0.2 + - - -
467A PHE* 2.7 27.5 + - - +
468A GLN 4.0 0.4 - - - -
469A ASN* 3.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN* 3.0 38.0 + - - +
132A LYS* 3.5 12.4 - - - +
134A ARG* 1.3 76.7 - - + +
136A ASP* 1.3 71.7 + - - +
138A LYS* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TRP* 2.9 31.5 + - + +
99A ASN* 4.2 1.4 + - - +
132A LYS* 2.6 55.2 + - - +
133A TRP 4.0 0.4 - - - +
135A GLN* 1.3 75.7 - - - +
137A ASN* 1.3 61.6 + - - +
138A LYS* 3.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 4.9 1.2 - - - -
88A MET* 4.1 24.3 - - - +
91A ASN* 3.5 27.7 + - + +
92A GLY* 3.8 9.3 - - - -
95A TRP* 3.6 16.8 - - - +
133A TRP* 2.8 64.4 + - + +
136A ASP* 1.3 75.5 - - - +
138A LYS* 1.3 73.5 + - - +
139A PHE* 3.2 3.9 + - - +
----------------------------------------------------------
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