Contacts of the helix formed by residues 5 - 27 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLN* 4.5 8.7 - - + +
4B PHE* 1.3 79.5 - - - +
6B ASP* 1.3 66.8 + - - +
7B ILE* 3.2 21.9 + - - +
8B ASP* 2.8 25.8 + - - +
9B LYS* 3.3 12.4 + - - +
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Residues in contact with ASP 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 1.3 76.8 - - - +
7B ILE* 1.3 57.2 + - - +
9B LYS* 3.1 24.9 + - - +
10B LEU* 2.8 28.9 + - - +
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 3.4 18.5 + - - +
6B ASP* 1.3 77.2 - - - +
8B ASP* 1.3 63.4 + - - +
10B LEU* 3.3 14.7 + - + +
11B ALA* 2.9 26.3 + - - +
292B GLU* 3.5 40.2 - - + +
293B VAL* 4.3 4.0 - - + +
296B HIS* 3.5 45.3 - - + +
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN 4.6 0.9 - - - +
4B PHE* 3.3 32.9 - - + -
5B THR* 2.8 33.9 + - - +
7B ILE* 1.3 78.9 - - - +
9B LYS* 1.3 65.6 + - - +
11B ALA* 3.2 4.4 + - - +
12B VAL* 3.0 27.4 + - - +
42B HIS* 2.8 31.4 + - + +
46B SER* 5.7 0.7 - - - -
224B LEU* 4.2 4.5 - - + -
296B HIS* 3.3 19.1 + - - -
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Residues in contact with LYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE 6.0 1.6 - - - -
5B THR 3.3 12.8 + - - +
6B ASP* 3.1 25.9 + - - +
8B ASP* 1.3 77.3 - - - +
10B LEU* 1.3 62.4 + - - +
12B VAL* 3.3 10.0 + - - +
13B SER* 3.1 25.4 + - - -
224B LEU* 4.8 13.0 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASP 2.8 12.7 + - - +
7B ILE* 3.5 21.1 - - + +
9B LYS* 1.3 78.1 - - - +
11B ALA* 1.3 61.8 + - - +
13B SER* 3.2 4.5 + - - +
14B THR* 2.8 28.4 + - - +
279B PHE 5.7 0.9 - - - +
281B PHE* 3.9 28.9 - - + -
290B PRO* 4.3 8.7 - - + -
292B GLU* 3.7 23.6 - - + +
293B VAL* 4.0 19.1 - - + -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 2.9 14.7 + - + +
8B ASP 3.5 8.3 - - - +
10B LEU* 1.3 76.9 - - - +
12B VAL* 1.3 57.2 + - - +
14B THR* 3.2 8.8 + - - -
15B ILE* 2.9 35.5 + - - +
42B HIS* 3.7 13.9 - - + -
80B LEU* 5.1 0.3 - - - +
293B VAL* 4.3 14.1 - - + +
296B HIS* 5.0 4.3 - - + -
297B TYR* 3.6 24.9 - - + +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 3.0 16.5 + - - +
9B LYS* 3.6 10.1 - - - +
11B ALA* 1.3 76.8 - - - +
13B SER* 1.3 57.7 + - - +
15B ILE* 3.4 9.3 + - - +
16B ARG* 3.0 53.8 + - - +
38B ALA* 4.2 1.6 - - + +
39B PRO* 3.9 32.5 - - + -
42B HIS* 3.9 25.6 - - + -
224B LEU* 4.3 13.0 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS 3.1 14.5 + - - -
10B LEU* 3.6 9.6 - - - -
12B VAL* 1.3 77.4 - - - +
14B THR* 1.3 57.4 + - - +
16B ARG* 3.3 8.7 + - - +
17B ILE* 3.0 37.5 + - - +
279B PHE* 3.8 32.8 + - - +
281B PHE* 3.8 19.1 - - - -
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU 2.8 17.5 + - - -
11B ALA* 3.4 11.2 - - - -
13B SER* 1.3 77.7 - - - +
15B ILE* 1.3 57.8 + - - +
17B ILE* 3.8 1.1 - - - +
18B LEU* 2.9 34.5 + - + +
80B LEU* 4.1 26.0 - - + -
281B PHE* 3.6 14.6 - - - -
288B VAL 3.8 21.0 - - - +
289B VAL* 4.2 3.1 - - + -
290B PRO* 3.6 17.7 - - + +
293B VAL* 3.5 18.4 - - + +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 2.9 19.2 + - - +
12B VAL* 3.6 7.4 - - - +
13B SER 3.3 0.2 - - - -
14B THR* 1.3 77.7 - - - +
16B ARG* 1.3 63.3 - - - +
18B LEU* 3.8 2.4 - - - +
19B ALA* 3.0 23.4 + - + +
38B ALA* 3.9 15.3 - - + +
42B HIS* 3.9 17.5 - - + -
73B LEU* 3.4 31.9 - - + -
76B SER* 4.1 7.1 + - - -
77B MET* 3.3 26.7 - - + -
80B LEU* 3.6 24.5 - - + -
297B TYR* 3.4 19.3 - - - +
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.0 29.3 + - - +
13B SER* 3.6 7.1 + - - +
15B ILE* 1.3 77.3 - - - +
17B ILE* 1.3 58.0 + - - +
19B ALA* 3.5 4.1 + - - +
20B VAL* 3.1 32.4 + - - +
34B PRO 5.3 0.9 - - - -
35B LEU* 2.9 42.2 + - + +
36B GLY 4.7 1.0 + - - -
38B ALA* 3.4 19.4 - - + +
39B PRO* 3.1 32.5 - - - +
221B ASN* 3.2 17.0 + - - +
252B TYR* 3.2 37.7 + - - +
279B PHE* 3.8 30.1 - - + -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER 3.0 17.0 + - - +
14B THR* 4.1 2.9 - - - +
16B ARG* 1.3 73.6 - - - +
18B LEU* 1.3 61.7 + - - +
20B VAL* 3.3 7.8 + - + +
21B ASP* 2.8 35.0 + - - +
272B VAL* 5.8 0.2 - - + -
275B LEU* 4.9 6.5 - - + -
276B LYS* 3.5 41.5 - - + -
279B PHE* 4.0 24.7 - - + -
281B PHE* 3.4 50.3 - - + -
288B VAL* 6.0 4.7 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 2.9 20.3 + - + +
15B ILE 3.8 3.1 - - - +
17B ILE* 1.3 75.8 - - - +
19B ALA* 1.3 58.7 + - - +
21B ASP* 3.4 4.3 + - - +
22B THR* 2.8 32.7 + - - -
76B SER* 3.6 22.2 - - - +
79B HIS* 4.4 7.6 - - + -
80B LEU* 4.0 28.0 - - + -
87B ILE* 4.0 10.8 - - + -
90B LEU* 3.7 25.8 - - + -
287B PHE* 3.7 36.3 - - + +
288B VAL 5.1 3.6 - - - +
289B VAL* 4.6 4.0 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE 3.0 17.7 + - - +
16B ARG* 3.8 4.7 - - - +
18B LEU* 1.3 75.8 - - - +
20B VAL* 1.3 64.0 + - + +
22B THR* 3.3 4.5 + - - -
23B VAL* 3.1 28.4 + - - +
31B PRO* 6.1 0.9 - - - -
34B PRO* 3.9 29.2 - - + -
72B ALA* 3.9 14.8 - - + +
73B LEU* 4.3 3.8 - - + +
76B SER* 3.4 14.3 + - - +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.1 18.7 + - - +
17B ILE* 3.3 7.6 + - + +
19B ALA* 1.3 78.4 - - + +
21B ASP* 1.3 56.3 + - - +
23B VAL* 3.2 7.3 + - - +
24B SER* 2.9 29.5 + - - +
31B PRO* 4.8 8.5 - - + +
35B LEU* 3.6 32.3 - - + -
267B LEU* 4.0 14.8 - - + +
272B VAL* 3.7 38.1 - - + -
275B LEU* 3.8 13.2 - - + -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 2.8 31.4 + - - +
18B LEU 3.8 4.5 - - - +
20B VAL* 1.3 73.1 - - - +
22B THR* 1.3 63.3 + - - +
24B SER* 3.8 6.6 - - - -
25B LYS* 2.9 20.6 + - - +
272B VAL* 4.1 7.3 - - - +
276B LYS* 2.8 29.8 + - - -
286B SER* 3.4 11.5 + - - -
287B PHE* 2.9 53.7 + - + +
288B VAL 4.7 0.3 + - - -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU 2.8 22.9 + - - -
19B ALA* 3.4 8.6 - - - -
21B ASP* 1.3 78.9 - - - +
23B VAL* 1.3 61.9 + - - +
25B LYS* 4.1 2.4 - - - +
26B ALA* 3.4 14.2 + - - +
72B ALA* 4.5 11.6 + - + +
75B TYR* 5.3 1.8 - - + -
76B SER* 4.7 1.0 + - - -
90B LEU* 3.5 31.6 - - + +
93B PHE* 3.4 44.2 - - + +
287B PHE* 3.6 18.5 - - - -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 3.1 15.4 + - - +
20B VAL* 3.7 7.4 - - - +
22B THR* 1.3 77.2 - - - +
24B SER* 1.3 59.1 + - - +
26B ALA 3.3 1.6 + - - -
27B ASN* 2.9 22.3 + - - -
28B SER 3.4 22.3 + - - +
29B GLY* 3.7 18.8 - - - +
30B HIS 4.0 17.7 - - - +
31B PRO* 4.2 10.3 - - + -
72B ALA* 3.7 20.6 - - + -
93B PHE* 4.1 10.3 - - + -
266B PRO* 3.8 21.0 - - + +
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Residues in contact with SER 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 2.9 18.3 + - - +
21B ASP* 3.3 9.4 + - - -
23B VAL* 1.3 76.8 - - - +
25B LYS* 1.3 63.0 + - - +
27B ASN* 2.9 16.8 + - - +
266B PRO* 4.0 8.1 - - - -
267B LEU 3.6 24.6 + - - -
272B VAL* 3.7 17.1 - - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP 2.9 17.2 + - - +
22B THR 4.1 2.7 - - - +
24B SER* 1.3 77.3 - - - +
26B ALA* 1.3 61.5 + - - +
27B ASN* 3.4 2.9 + - - +
90B LEU 5.7 0.2 - - - +
91B LYS* 2.9 46.2 + - + +
92B GLN* 4.5 7.9 - - - +
287B PHE* 3.7 29.4 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 4.9 1.9 - - - +
641A LYS* 4.4 10.1 + - - -
22B THR 3.4 10.5 + - - +
23B VAL 3.3 3.7 + - - +
24B SER 3.2 0.4 - - - -
25B LYS* 1.3 77.3 - - - +
27B ASN* 1.3 73.3 + - - +
28B SER* 3.1 24.6 + - - +
93B PHE* 3.4 31.2 - - + +
94B ARG* 4.3 4.7 - - + -
95B GLN* 4.2 16.8 + - - +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 5.4 0.2 - - - +
641A LYS* 5.6 3.4 - - - +
23B VAL 2.9 4.2 + - - -
24B SER 2.9 17.6 + - - +
25B LYS 4.4 2.5 - - - +
26B ALA* 1.3 80.1 - - - +
28B SER* 1.3 59.8 + - - +
266B PRO* 3.5 25.4 - - - +
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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