Contacts of the helix formed by residues 3 - 23 (chain A) in PDB entry 1XGS
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 THR 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.4 0.2 + - - -
2A ASP* 1.3 72.1 + - - +
4A GLU* 1.3 58.5 + - - +
5A LYS 3.4 0.2 - - - -
6A LEU* 3.3 13.8 + - + +
7A MET* 2.7 44.6 + - - +
181A GLY* 6.4 1.3 - - - -
284A ILE* 4.3 27.8 - - + -
291A ILE* 5.7 5.8 - - + -
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Residues in contact with GLU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASP* 3.0 24.0 - - + +
3A THR* 1.3 80.3 + - - +
5A LYS* 1.3 62.0 + - + +
7A MET* 3.6 7.8 - - + +
8A LYS* 2.8 30.0 + - - +
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Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 27.7 - - - +
2A ASP* 3.5 13.9 + - + +
3A THR 3.4 0.4 - - - -
4A GLU* 1.3 78.8 - - + +
6A LEU* 1.3 52.4 + - - +
8A LYS* 3.2 6.8 + - - +
9A ALA* 2.8 35.5 + - - +
87A ILE* 3.9 25.8 - - + +
88A ASP* 3.5 27.2 + - + +
90A PHE* 3.5 39.3 - - + -
157A ARG* 4.5 5.9 - - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASP 3.6 10.9 + - - +
3A THR* 3.3 14.3 + - + +
4A GLU 3.3 0.4 - - - -
5A LYS* 1.3 77.1 - - - +
7A MET* 1.3 56.8 + - - +
9A ALA* 3.3 4.5 + - - +
10A GLY* 3.0 25.6 + - - -
90A PHE* 3.9 31.9 - - + -
91A ILE 3.3 28.2 - - - +
92A ALA* 4.7 1.4 - - - +
155A ILE* 5.8 1.3 - - + -
183A VAL* 3.6 38.1 - - + -
282A THR* 5.6 0.9 - - + -
284A ILE* 4.0 21.1 - - + -
293A THR* 4.1 9.4 + - + -
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Residues in contact with MET 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 2.7 33.2 + - - +
4A GLU* 3.6 8.5 - - - +
6A LEU* 1.3 69.5 - - - +
8A LYS* 1.3 65.0 + - - +
10A GLY* 3.4 1.4 + - - -
11A GLU* 3.0 24.4 + - - +
284A ILE* 4.5 4.3 - - - -
291A ILE* 3.7 36.1 - - + -
292A VAL 5.5 0.7 - - - +
293A THR* 4.0 22.6 - - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU 2.8 18.2 + - - +
5A LYS* 3.5 7.0 - - - +
7A MET* 1.3 74.2 - - - +
9A ALA* 1.3 66.6 + - - +
11A GLU* 3.2 24.2 + - - +
12A ILE* 3.2 41.7 + - + +
44A LEU 4.4 8.6 + - - -
45A GLY* 4.8 6.9 + - - -
87A ILE* 3.8 26.1 - - + +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS 2.8 16.9 + - - +
6A LEU 3.7 4.7 - - - +
8A LYS* 1.3 73.4 - - - +
10A GLY* 1.3 57.3 + - - +
12A ILE* 3.5 0.9 + - - +
13A ALA* 3.0 23.2 + - - +
85A VAL* 3.6 27.3 - - - +
87A ILE* 3.8 13.7 - - + +
90A PHE 3.4 26.2 - - - +
91A ILE 4.2 0.4 - - - -
92A ALA* 3.3 13.4 - - + +
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Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU 3.0 13.8 + - - -
7A MET 3.4 1.8 + - - -
8A LYS 3.2 0.2 - - - -
9A ALA* 1.3 75.5 - - - +
11A GLU* 1.3 58.6 + - - +
13A ALA* 3.7 1.6 - - - +
14A LYS* 2.9 31.0 + - - +
92A ALA* 3.3 15.0 - - - +
293A THR* 3.3 27.2 - - - +
294A THR* 3.9 4.0 - - - -
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET 3.0 12.7 + - - +
8A LYS* 3.2 27.8 + - - +
10A GLY* 1.3 75.5 - - - +
12A ILE* 1.3 62.0 + - - +
14A LYS* 3.4 10.5 + - + +
15A LYS* 3.1 62.6 + - + +
293A THR 3.8 2.1 + - - -
295A GLU 6.0 0.7 - - - -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 3.2 31.2 + - + +
9A ALA 3.8 6.3 - - - +
11A GLU* 1.3 81.6 - - - +
13A ALA* 1.3 65.6 + - - +
15A LYS* 3.4 4.2 + - + +
16A VAL* 3.0 28.4 + - + +
41A ILE* 4.2 8.3 - - - +
44A LEU* 3.6 52.0 - - + +
45A GLY 4.1 0.7 - - - -
46A GLY* 3.8 20.0 - - - +
85A VAL* 4.0 20.0 - - + -
87A ILE* 4.3 7.2 - - + -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 3.0 17.8 + - - +
10A GLY 3.3 4.2 + - - +
12A ILE* 1.3 75.6 - - - +
14A LYS* 1.3 59.3 + - - +
16A VAL* 3.8 3.7 - - - +
17A ARG* 2.8 31.2 + - - +
83A VAL* 4.0 8.7 - - + +
85A VAL* 3.9 16.8 - - + -
92A ALA* 3.9 19.3 - - + +
94A THR* 3.8 20.9 - - + -
294A THR* 4.3 1.1 - - + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY 2.9 17.7 + - - +
11A GLU* 3.6 9.4 - - + +
13A ALA* 1.3 74.4 - - - +
15A LYS* 1.3 65.1 + - + +
17A ARG* 3.0 30.2 + - - +
18A GLU* 2.8 49.2 + - + +
294A THR 3.8 11.9 + - - +
295A GLU* 3.4 29.8 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.1 49.2 + - + +
12A ILE* 3.8 5.5 - - + +
14A LYS* 1.3 91.7 - - + +
16A VAL* 1.3 57.3 + - - +
18A GLU* 3.2 6.8 + - - +
19A LYS* 3.0 27.6 + - - +
40A MET* 4.9 2.6 - - - +
44A LEU* 4.2 31.4 - - + +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.0 18.4 + - + +
13A ALA* 3.8 4.3 - - - +
15A LYS* 1.3 75.6 - - - +
17A ARG* 1.3 62.7 + - - +
19A LYS* 3.2 3.5 + - - +
20A ALA* 2.9 26.9 + - - +
37A ILE* 3.2 34.5 - - + +
40A MET* 3.8 22.0 - - + -
41A ILE* 3.7 28.3 - - + +
44A LEU* 3.7 20.0 - - + -
83A VAL* 4.6 9.2 - - + -
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 2.8 20.2 + - - +
14A LYS* 3.4 22.8 - - - +
16A VAL* 1.3 77.4 - - - +
18A GLU* 1.3 90.0 + - - +
20A ALA* 3.2 8.2 + - - +
21A ILE* 3.2 23.2 + - + +
81A ILE* 5.3 4.3 - - + +
83A VAL* 4.2 12.6 - - + -
94A THR* 2.9 38.6 + - + +
95A ALA* 4.4 7.0 - - - -
96A VAL* 4.0 32.7 - - + +
281A HIS* 3.9 10.0 - - - -
294A THR 2.7 29.3 + - - -
295A GLU* 4.6 5.3 + - - +
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 2.8 35.8 + - + +
15A LYS* 3.7 6.1 - - - +
17A ARG* 1.3 111.3 + - - +
19A LYS* 1.3 63.1 + - - +
21A ILE* 3.5 28.1 + - - +
22A LYS* 3.6 16.8 + - - +
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS 3.0 12.3 + - - +
16A VAL 3.5 8.5 - - - +
17A ARG 3.1 0.2 - - - -
18A GLU* 1.3 75.6 - - - +
20A ALA* 1.3 64.3 + - - +
22A LYS* 3.0 20.2 + - + +
23A LEU* 3.2 34.2 + - + +
36A SER* 6.4 0.7 - - - -
40A MET* 3.1 43.1 - - + +
43A GLU* 5.4 3.6 + - - -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL 2.9 9.8 + - - +
17A ARG* 3.2 11.0 + - - +
19A LYS* 1.3 76.9 - - - +
21A ILE* 1.3 60.8 + - - +
23A LEU* 3.3 3.2 + - - +
24A ALA* 3.1 23.6 + - - +
33A LEU* 4.2 10.5 - - + +
37A ILE* 3.4 30.0 - - + +
81A ILE* 3.9 32.1 - - + +
83A VAL* 5.5 0.2 - - + -
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.2 13.1 + - + +
18A GLU* 3.7 34.5 - - - +
19A LYS 3.1 0.8 - - - -
20A ALA* 1.3 76.2 - - - +
22A LYS* 1.3 78.9 + - - +
24A ALA* 3.2 19.5 + - - +
81A ILE* 4.3 5.4 - - + -
96A VAL* 3.8 39.3 - - + -
98A VAL* 4.0 22.8 - - + +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU 3.8 12.1 - - - +
19A LYS* 3.0 11.7 + - + +
21A ILE* 1.3 97.7 - - - +
23A LEU* 1.3 64.3 + - + +
24A ALA 3.6 0.7 + - - -
25A ARG* 4.7 13.7 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 3.2 35.8 + - + +
20A ALA 3.3 2.0 + - - +
21A ILE 3.2 0.2 - - - -
22A LYS* 1.3 79.7 - - + +
24A ALA* 1.3 60.7 + - - +
25A ARG* 2.8 31.3 + - - +
28A MET* 3.3 35.1 - - + +
33A LEU* 3.6 27.6 - - + -
36A SER* 4.4 20.9 - - - +
37A ILE* 4.6 5.8 - - + -
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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) + - + + + + + -
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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