Contacts of the helix formed by residues 5 - 27 (chain A) in PDB entry 1GPU
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 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 4.5 8.3 - - + +
4A PHE* 1.3 80.4 - - - +
6A ASP* 1.3 67.3 + - - +
7A ILE* 3.2 21.5 + - - +
8A ASP* 2.7 27.1 + - - +
9A LYS* 3.3 13.2 + - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 1.3 77.9 - - - +
7A ILE* 1.3 56.1 + - - +
9A LYS* 3.1 25.5 + - + +
10A LEU* 2.8 29.0 + - - +
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Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 3.4 17.3 + - - +
6A ASP* 1.3 77.9 - - - +
8A ASP* 1.3 65.0 + - - +
10A LEU* 3.3 15.8 + - + -
11A ALA* 2.9 26.2 + - + +
292A GLU* 3.6 39.0 - - + +
293A VAL* 4.4 4.3 - - + +
296A HIS* 3.5 47.1 - - + +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN 4.5 1.4 - - - +
4A PHE* 3.2 31.1 - - + -
5A THR* 2.7 35.1 + - - +
7A ILE* 1.3 85.5 - - - +
9A LYS* 1.3 64.7 + - - +
11A ALA* 3.2 3.1 + - - +
12A VAL* 3.0 28.0 + - - +
42A HIS* 2.8 33.5 + - + +
46A SER* 5.2 1.0 + - - -
224A LEU* 4.2 4.9 - - + -
296A HIS* 3.4 14.8 + - - -
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE 6.1 1.3 - - - -
5A THR 3.3 11.4 + - - +
6A ASP* 3.1 25.6 + - - +
8A ASP* 1.3 76.9 - - - +
10A LEU* 1.3 62.4 + - - +
12A VAL* 3.4 9.9 + - - +
13A SER* 3.1 25.5 + - - -
224A LEU* 4.7 13.5 - - + -
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Residues in contact with LEU 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 ASP 2.8 13.4 + - - +
7A ILE* 3.5 25.6 - - + +
8A ASP 3.2 0.2 - - - -
9A LYS* 1.3 76.2 - - - +
11A ALA* 1.3 58.6 + - - +
13A SER* 3.3 4.2 + - - +
14A THR* 2.9 32.3 + - - +
279A PHE 5.7 0.2 - - - +
281A PHE* 3.9 28.7 - - + -
290A PRO* 4.3 10.3 - - + -
292A GLU* 3.8 22.9 - - + +
293A VAL* 4.0 14.1 - - + -
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 2.9 14.0 + - + +
8A ASP 3.2 8.5 + - - +
10A LEU* 1.3 77.6 - - - +
12A VAL* 1.3 56.6 + - - +
14A THR* 3.2 4.2 + - - -
15A ILE* 2.9 34.6 + - - +
42A HIS* 3.7 13.9 - - + -
80A LEU* 5.1 0.2 - - - +
293A VAL* 4.2 17.4 - - + +
296A HIS* 5.0 4.5 - - + -
297A TYR* 3.6 27.6 - - + +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP 3.0 15.7 + - - +
9A LYS* 3.6 10.1 - - - +
10A LEU 3.2 0.2 - - - -
11A ALA* 1.3 76.6 - - - +
13A SER* 1.3 62.5 + - - +
15A ILE* 3.3 10.1 + - - +
16A ARG* 3.0 48.9 + - - +
38A ALA* 4.3 1.8 - - + +
39A PRO* 4.0 30.5 - - + -
42A HIS* 3.9 26.0 - - + -
224A LEU* 4.4 13.5 - - + -
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 3.1 13.9 + - - -
10A LEU* 3.3 9.1 + - - -
12A VAL* 1.3 76.4 - - - +
14A THR* 1.3 64.3 + - - +
16A ARG* 3.4 6.9 + - - +
17A ILE* 3.0 31.2 + - - +
279A PHE* 3.6 33.5 + - - +
281A PHE* 3.7 21.8 - - - -
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 2.9 14.9 + - - -
11A ALA* 3.2 11.9 + - - -
13A SER* 1.3 78.1 - - - +
15A ILE* 1.3 57.6 + - - +
17A ILE* 3.5 1.1 + - - +
18A LEU* 2.9 33.9 + - + +
80A LEU* 4.1 26.5 - - + -
281A PHE* 3.5 13.9 - - - -
288A VAL 3.8 20.7 - - - +
289A VAL* 4.3 4.3 - - + -
290A PRO* 3.5 23.8 - - + +
293A VAL* 3.6 10.0 - - + +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 2.9 19.2 + - - +
12A VAL* 3.6 6.7 - - - +
14A THR* 1.3 74.8 - - - +
16A ARG* 1.3 64.0 + - - +
18A LEU* 3.3 3.0 + - - +
19A ALA* 3.0 24.1 + - + +
38A ALA* 3.9 14.8 - - + +
42A HIS* 3.9 20.2 - - + -
73A LEU* 3.5 32.5 - - + -
76A SER* 4.2 6.3 + - - -
77A MET* 3.4 24.5 - - - -
80A LEU* 3.6 24.5 - - + -
297A TYR* 3.5 19.5 - - - +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.0 28.3 + - - +
13A SER* 3.6 6.7 + - - +
15A ILE* 1.3 78.8 - - - +
17A ILE* 1.3 56.7 + - - +
19A ALA* 3.7 4.3 - - - +
20A VAL* 3.1 31.5 + - - +
34A PRO 5.2 0.9 - - - -
35A LEU* 2.8 45.6 + - + +
36A GLY 4.8 1.0 + - - -
38A ALA* 3.4 19.6 - - + +
39A PRO* 3.2 29.5 - - - +
221A ASN* 3.3 13.7 + - - +
252A TYR* 3.1 41.7 + - - +
275A LEU* 5.5 0.2 - - - -
279A PHE* 3.8 31.4 - - + -
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.0 17.0 + - - +
14A THR* 4.1 3.1 - - - +
16A ARG* 1.3 73.3 - - - +
18A LEU* 1.3 61.6 + - - +
20A VAL* 3.3 7.4 + - + +
21A ASP* 2.8 34.2 + - - +
275A LEU* 4.9 6.7 - - + -
276A LYS* 3.6 43.1 - - + -
279A PHE* 4.0 22.4 - - + -
281A PHE* 3.3 50.5 - - + -
288A VAL* 6.0 5.4 - - + +
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Residues in contact with LEU 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 THR* 2.9 20.3 + - + +
15A ILE 3.8 3.4 - - - +
17A ILE* 1.3 76.7 - - - +
19A ALA* 1.3 54.1 + - - +
21A ASP* 3.4 3.7 + - - +
22A THR* 2.7 37.0 + - - -
76A SER* 3.6 21.5 - - - +
79A HIS* 4.4 8.3 - - + -
80A LEU* 4.0 27.4 - - + -
87A ILE* 3.9 11.2 - - + -
90A LEU* 3.6 24.5 - - + -
287A PHE* 3.7 37.2 - - + +
288A VAL 5.5 3.8 + - - +
289A VAL* 4.6 4.0 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.0 17.8 + - + +
16A ARG* 3.7 5.8 - - - +
18A LEU* 1.3 77.8 - - - +
20A VAL* 1.3 62.0 + - + +
22A THR* 3.3 4.6 + - - -
23A VAL* 3.1 29.1 + - - +
31A PRO* 6.1 0.7 - - - -
34A PRO* 3.9 28.5 - - + -
72A ALA* 3.9 15.2 - - + +
73A LEU* 4.4 2.9 - - - +
76A SER* 3.4 14.3 + - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 3.1 21.2 + - - +
17A ILE* 3.6 8.3 - - + +
19A ALA* 1.3 76.8 - - + +
21A ASP* 1.3 57.6 + - - +
23A VAL* 3.2 7.7 + - - +
24A SER* 2.8 28.8 + - - +
31A PRO* 4.7 9.0 - - + +
34A PRO* 6.5 0.2 - - + -
35A LEU* 3.6 31.6 - - + -
267A LEU* 4.1 13.9 - - + +
272A VAL* 3.9 37.7 - - + -
275A LEU* 3.8 15.0 - - + -
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Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 2.8 29.1 + - - +
18A LEU* 3.8 4.0 - - - +
20A VAL* 1.3 73.1 - - - +
22A THR* 1.3 58.5 + - - +
24A SER* 3.8 6.6 - - - -
25A LYS* 2.9 26.7 + - - +
272A VAL* 4.1 7.8 - - - +
276A LYS* 2.9 32.6 + - - -
286A SER* 3.3 12.8 + - - -
287A PHE* 2.9 51.5 + - + +
288A VAL 4.7 0.2 + - - -
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Residues in contact with THR 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 LEU 2.7 22.8 + - - -
19A ALA* 3.4 9.3 - - - -
21A ASP* 1.3 79.6 - - - +
23A VAL* 1.3 61.8 + - - +
25A LYS* 3.6 2.4 + - - +
26A ALA* 3.4 14.6 + - - +
72A ALA* 4.6 11.2 - - + +
75A TYR* 5.4 2.9 - - + -
76A SER* 4.7 1.0 + - - -
90A LEU* 3.5 28.8 - - + +
93A PHE* 3.4 43.8 - - + +
287A PHE* 3.6 18.2 - - - -
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.1 15.0 + - + +
20A VAL 3.7 5.8 - - - +
22A THR* 1.3 73.8 - - - +
24A SER* 1.3 59.2 + - - +
26A ALA 3.3 1.7 + - - -
27A ASN* 3.0 22.9 + - - -
28A SER 3.4 23.1 + - - +
29A GLY 3.7 16.6 - - - +
30A HIS 4.0 21.1 - - - +
31A PRO* 4.1 11.7 - - + -
72A ALA* 3.8 20.9 - - + -
93A PHE* 4.2 6.5 - - + -
266A PRO* 3.8 22.4 - - + +
267A LEU 5.3 0.2 - - - +
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 2.8 18.0 + - - +
21A ASP* 3.8 8.7 - - - -
23A VAL* 1.3 77.2 - - - +
25A LYS* 1.3 63.4 + - - +
27A ASN* 2.9 16.6 + - - +
266A PRO* 4.1 8.5 - - - +
267A LEU 3.6 24.4 + - - -
272A VAL* 3.7 18.6 - - - +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP 2.9 18.2 + - - +
22A THR 4.0 2.7 - - - +
24A SER* 1.3 77.4 - - - +
26A ALA* 1.3 61.1 + - - +
27A ASN* 3.4 2.9 + - - +
90A LEU 5.7 0.2 - - - +
91A LYS* 2.9 49.2 + - + +
92A GLN* 4.4 8.3 - - - +
287A PHE* 3.7 26.2 - - + -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR 3.4 10.5 + - - +
23A VAL 3.3 3.5 + - - +
24A SER 3.2 0.6 - - - -
25A LYS* 1.3 77.6 - - - +
27A ASN* 1.3 71.8 + - - +
28A SER* 3.1 24.2 + - - +
93A PHE* 3.4 31.4 - - + +
94A ARG* 4.3 4.7 - - + -
95A GLN* 4.2 12.5 + - - +
476B GLU* 4.9 1.6 - - - +
641B LYS* 4.3 13.7 + - - -
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL 3.0 4.0 + - - -
24A SER 2.9 18.3 + - - +
25A LYS 4.5 2.5 - - - +
26A ALA* 1.3 79.3 - - - +
28A SER* 1.3 59.4 + - - +
266A PRO* 3.6 24.5 - - - +
476B GLU* 5.5 0.2 - - - +
641B LYS* 5.6 3.6 - - - +
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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