Contacts of the strand formed by residues 6 - 24 (chain B) in PDB entry 2PGW
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 ILE 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 1.3 72.9 - - - +
7B SER* 1.3 61.5 + - - +
8B ASN 3.7 10.3 - - - +
9B VAL* 4.1 6.7 - - + -
39B ILE* 3.5 36.3 - - + -
40B GLU 3.5 8.7 - - - +
41B ALA* 4.1 1.6 - - - +
71B LEU* 3.5 34.3 - - + +
72B VAL* 3.9 8.6 - - - +
73B GLY* 2.7 28.9 + - - -
74B HIS* 2.8 19.2 + - + +
76B PRO* 4.1 15.3 - - + -
113B MSE 3.6 29.4 - - + -
116B LEU* 4.5 1.6 - - + -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS 3.4 1.0 + - - -
6B ILE* 1.3 74.5 - - - +
8B ASN* 1.3 83.3 + - - +
40B GLU* 2.7 22.7 + - - +
41B ALA 3.5 11.1 + - - -
42B ASP* 3.9 21.4 - - - -
72B VAL* 3.4 19.2 - - - +
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Residues in contact with ASN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.7 2.2 - - - +
7B SER* 1.3 110.4 + - - +
9B VAL* 1.3 70.5 + - - +
10B ARG* 4.1 20.8 - - - +
39B ILE* 3.7 0.2 - - - -
40B GLU* 2.8 34.7 + - + +
72B VAL* 4.5 4.7 - - - -
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.1 16.2 - - + -
8B ASN* 1.3 84.7 - - - +
10B ARG* 1.3 63.8 + - - +
37B ILE* 4.5 1.6 - - + -
38B GLU 3.2 9.0 - - - +
39B ILE* 4.2 13.9 - - + -
65B TYR* 3.9 15.6 + - + -
68B ALA* 3.6 31.9 - - + +
69B LYS* 3.9 35.4 - - + +
71B LEU* 4.7 2.2 - - + -
72B VAL* 4.2 9.4 - - + +
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Residues in contact with ARG 10 (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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8B ASN* 4.1 18.7 - - - +
9B VAL* 1.3 76.2 - - - +
11B VAL* 1.3 64.7 + - - +
12B ARG* 4.5 12.8 - - + +
36B LEU 3.7 0.3 - - - +
37B ILE* 3.5 5.0 - - - +
38B GLU* 2.9 79.4 + - + +
40B GLU* 2.9 31.7 + - - +
46B VAL* 4.4 10.7 - - - +
65B TYR* 4.9 4.0 - - - -
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Residues in contact with VAL 11 (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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10B ARG* 1.3 75.7 - - - +
12B ARG* 1.3 70.0 + - - +
13B PRO* 3.6 9.2 - - + +
35B ASN* 4.4 5.8 - - + -
36B LEU 3.2 9.0 - - - +
37B ILE* 4.2 8.1 - - + -
61B ALA* 3.9 29.6 - - + +
64B LEU* 3.9 23.1 - - + -
65B TYR* 3.6 46.5 - - + +
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Residues in contact with ARG 12 (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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10B ARG* 4.5 13.6 - - + +
11B VAL* 1.3 81.0 - - - +
13B PRO* 1.3 66.6 - - - +
14B LEU* 3.4 14.6 + - + +
35B ASN* 4.4 0.7 - - - -
36B LEU* 2.9 41.4 + - + +
38B GLU* 2.8 43.1 + - - -
360B LEU* 5.8 2.4 - - - +
362B GLU* 5.3 2.2 + - - +
365B VAL* 3.5 23.2 - - - +
366B ALA* 4.9 3.0 - - - +
369B GLU* 3.1 41.1 + - - +
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Residues in contact with PRO 13 (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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11B VAL* 3.6 10.3 - - + +
12B ARG* 1.3 83.2 - - - +
14B LEU* 1.3 66.4 + - - +
35B ASN* 3.4 22.7 - - - +
57B GLN* 3.6 5.2 - - + +
61B ALA* 3.9 19.7 - - + -
369B GLU* 3.7 10.5 - - + +
372B TYR* 3.4 53.0 - - + +
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Residues in contact with LEU 14 (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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12B ARG* 3.5 14.8 - - + +
13B PRO* 1.3 83.1 - - - +
15B VAL* 1.3 63.7 + - - +
16B LEU* 4.2 17.5 - - + -
33B ALA* 3.0 15.1 - - - +
34B VAL* 2.8 28.6 + - + +
36B LEU* 3.5 28.9 - - + -
57B GLN* 2.9 16.5 + - - +
335B ILE* 3.9 16.6 - - + -
365B VAL* 3.5 24.5 - - + +
368B GLY 3.7 4.0 - - - -
369B GLU* 3.5 26.0 - - + +
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Residues in contact with VAL 15 (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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14B LEU* 1.3 79.8 - - - +
16B LEU* 1.3 69.1 + - - +
31B SER* 3.8 20.6 - - - +
32B PHE 3.6 6.5 - - - +
33B ALA* 4.2 3.6 - - + -
57B GLN* 3.8 14.1 - - - +
368B GLY* 3.3 8.8 + - - -
371B ARG* 3.0 48.3 + - + +
372B TYR* 3.6 22.0 - - - +
375B SER* 4.2 10.5 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.3 9.9 - - + -
15B VAL* 1.3 84.9 - - - +
17B PRO* 1.3 70.6 - - + +
18B LEU* 4.6 1.0 - - - +
31B SER* 3.0 15.5 - - - -
32B PHE* 2.9 31.2 + - + +
34B VAL* 4.5 8.7 - - + -
303B THR* 3.4 34.8 - - + -
331B VAL* 4.1 23.1 - - + +
333B GLU 5.3 3.6 - - - +
335B ILE* 4.1 28.3 - - + +
364B LEU 4.6 4.0 - - - +
368B GLY* 4.0 16.8 - - - -
371B ARG* 5.3 0.9 - - - +
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 5.9 0.2 - - + -
16B LEU* 1.3 88.4 - - + +
18B LEU* 1.3 64.4 + - - +
30B GLU 3.7 3.4 - - - +
31B SER* 3.4 12.1 - - - -
331B VAL* 3.6 6.8 - - + +
332B GLN* 3.0 34.0 + - + +
333B GLU 6.2 0.4 - - - +
371B ARG* 3.2 46.9 - - - +
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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
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17B PRO* 1.3 78.9 - - - +
19B LYS* 1.3 66.4 + - - +
20B GLN* 3.3 15.2 + - - +
22B TYR* 3.8 20.2 - - + -
29B ARG* 3.5 24.9 - - + +
30B GLU 3.0 15.1 + - - +
31B SER* 3.6 17.5 - - - +
32B PHE* 3.3 47.3 - - + -
330B LEU* 3.2 25.1 - - + +
331B VAL* 4.1 3.1 - - - -
332B GLN* 3.9 12.2 + - - +
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Residues in contact with LYS 19 (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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18B LEU* 1.3 73.2 - - - +
20B GLN* 1.3 66.3 + - + +
328B TRP* 6.0 3.7 - - - -
329B GLN* 3.2 30.3 + - - +
330B LEU* 3.0 14.4 + - - +
331B VAL 3.5 21.5 - - - +
332B GLN* 3.5 29.2 + - - +
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Residues in contact with GLN 20 (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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18B LEU* 3.3 19.6 - - - +
19B LYS* 1.3 82.3 - - + +
21B PRO* 1.3 89.0 + - + +
22B TYR* 3.4 2.3 + - - +
30B GLU* 5.5 1.1 - - - -
144B GLN* 4.3 26.9 - - - +
145B GLY* 5.5 2.8 - - - +
330B LEU* 6.4 2.2 - - + -
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Residues in contact with PRO 21 (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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20B GLN* 1.3 102.3 + - + +
22B TYR* 1.3 59.8 + - - +
23B HIS* 3.9 22.2 + - + -
28B ILE* 3.2 29.4 - - + -
29B ARG 3.8 7.2 - - - +
30B GLU* 4.5 16.1 - - + +
144B GLN* 5.2 2.6 + - - -
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Residues in contact with TYR 22 (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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18B LEU* 3.8 17.5 - - + -
20B GLN 3.4 0.9 + - - +
21B PRO* 1.3 72.1 - - - +
23B HIS* 1.3 77.5 + - - +
24B TRP* 3.7 5.0 + - + -
28B ILE* 3.5 2.5 - - - -
29B ARG* 2.8 72.4 + - + +
32B PHE* 6.3 1.3 - + - -
142B PHE* 3.6 29.2 - + - -
144B GLN* 3.5 29.6 - - - +
169B LYS* 5.9 3.1 - - - +
301B PHE* 3.5 33.9 - + - -
327B MSE 4.5 0.2 - - - +
330B LEU* 4.3 15.7 - - + -
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Residues in contact with HIS 23 (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 PRO* 3.9 26.9 + - + -
22B TYR* 1.3 85.2 - - - +
24B TRP* 1.3 61.6 + - - +
27B GLY 3.6 5.8 - - - +
28B ILE* 4.0 23.3 - - + +
144B GLN* 5.7 0.6 - - - +
146B GLU* 3.5 48.7 + - + +
169B LYS* 5.5 7.3 - - - +
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Residues in contact with TRP 24 (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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22B TYR* 3.8 17.0 - - + -
23B HIS* 1.3 75.6 - - - +
25B SER* 1.3 69.5 + - - +
26B TYR* 2.9 55.8 + + + -
27B GLY* 3.1 33.1 + - - +
28B ILE 3.6 16.1 + - - -
29B ARG* 3.5 40.9 - - + +
169B LYS* 6.3 1.8 - - - +
89F GLN* 3.3 36.6 - - + -
93F GLY* 3.9 20.6 - - - +
94F HIS* 4.0 10.8 - + - -
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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
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Atomic class I II III IV V VI VII VIII
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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