Contacts of the strand formed by residues 6 - 24 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS* 1.3 72.9 - - - +
7H SER* 1.3 62.0 + - - +
8H ASN 3.9 10.1 - - - +
9H VAL* 4.3 4.9 - - + -
39H ILE* 3.5 27.1 - - + -
40H GLU 3.6 7.9 - - - +
41H ALA* 4.2 2.0 - - - +
71H LEU* 3.5 34.1 - - + +
72H VAL* 3.6 8.1 - - - +
73H GLY* 2.8 28.6 + - - -
74H HIS* 2.8 19.5 + - + +
75H SER 4.5 0.7 - - - -
76H PRO* 4.3 13.9 - - + -
113H MSE 3.6 37.7 - - + -
116H LEU* 4.6 5.6 - - + -
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Residues in contact with SER 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS 3.3 1.4 + - - -
6H ILE* 1.3 73.9 - - - +
8H ASN* 1.3 82.6 + - - +
40H GLU* 2.7 24.0 + - - +
41H ALA 3.0 14.0 + - - -
42H ASP* 3.8 19.9 - - - -
72H VAL* 3.6 17.8 - - - +
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Residues in contact with ASN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 3.8 2.6 - - - +
7H SER* 1.3 103.8 + - - +
9H VAL* 1.3 72.0 + - - +
10H ARG* 4.8 9.6 - - + +
38H GLU 4.4 0.2 - - - -
39H ILE* 3.5 0.5 - - - -
40H GLU* 2.8 58.7 + - + +
72H VAL* 4.7 4.5 - - - -
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Residues in contact with VAL 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 4.3 10.8 - - + -
8H ASN* 1.3 82.6 - - - +
10H ARG* 1.3 65.3 + - - +
37H ILE* 4.4 2.5 - - + -
38H GLU 3.1 10.1 - - - +
39H ILE* 4.5 9.9 - - + -
65H TYR* 3.9 17.7 + - + -
68H ALA* 3.6 32.1 - - + +
69H LYS* 4.0 36.6 - - + +
71H LEU* 4.7 2.2 - - + -
72H VAL* 4.2 13.4 - - + +
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Residues in contact with ARG 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ASN* 4.8 7.4 - - + +
9H VAL* 1.3 83.8 - - - +
11H VAL* 1.3 63.5 + - - +
12H ARG* 4.2 8.9 + - + +
36H LEU 3.7 0.5 - - - +
37H ILE* 3.4 4.8 - - - +
38H GLU* 2.6 82.3 + - - +
40H GLU* 2.6 44.1 + - - +
46H VAL* 4.2 14.6 - - - +
65H TYR* 5.0 3.1 - - - -
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Residues in contact with VAL 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ARG* 1.3 78.6 - - - +
12H ARG* 1.3 64.4 + - - +
13H PRO* 3.6 11.4 - - + +
35H ASN* 4.5 4.5 - - + -
36H LEU 3.2 9.4 - - - +
37H ILE* 4.2 8.5 - - + -
61H ALA* 4.0 26.0 - - + +
64H LEU* 3.8 25.6 - - + -
65H TYR* 3.6 47.6 - - + +
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Residues in contact with ARG 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ARG* 4.7 6.7 - - + +
11H VAL* 1.3 82.7 - - - +
13H PRO* 1.3 67.9 - - - +
14H LEU* 3.5 11.4 - - + +
35H ASN* 4.5 0.4 - - - -
36H LEU* 3.0 42.4 + - + +
38H GLU* 2.7 51.8 + - - +
360H LEU* 5.6 2.4 - - - +
362H GLU* 2.9 38.2 + - - -
365H VAL* 3.4 17.6 - - - +
369H GLU* 2.8 47.2 + - - +
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Residues in contact with PRO 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H VAL* 3.6 10.8 - - + +
12H ARG* 1.3 84.3 - - - +
14H LEU* 1.3 66.2 + - - +
35H ASN* 3.3 25.4 - - - +
57H GLN* 3.7 7.0 - - + +
61H ALA* 4.0 19.1 - - + -
369H GLU* 3.6 9.2 - - + +
372H TYR* 3.6 48.3 - - + +
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ARG* 3.5 15.0 - - + +
13H PRO* 1.3 85.1 - - - +
15H VAL* 1.3 64.4 + - - +
16H LEU* 4.2 19.1 - - + -
33H ALA* 3.2 2.9 - - - +
34H VAL* 2.8 39.6 + - + +
36H LEU* 3.6 31.6 - - + -
57H GLN* 3.0 16.8 + - - +
335H ILE* 4.1 15.0 - - + -
365H VAL* 3.7 21.3 - - + +
368H GLY 3.6 4.5 - - - -
369H GLU* 3.4 26.9 - - + +
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Residues in contact with VAL 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 1.3 79.0 - - - +
16H LEU* 1.3 65.5 + - - +
31H SER* 3.8 22.7 - - - +
32H PHE 3.6 5.6 - - - +
33H ALA* 4.6 4.9 - - + -
57H GLN* 3.8 14.4 - - - +
368H GLY* 3.2 8.1 + - - -
371H ARG* 3.2 46.2 + - + -
372H TYR* 3.7 23.3 - - + -
375H SER* 4.4 8.5 - - - +
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Residues in contact with LEU 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 4.2 11.9 - - + -
15H VAL* 1.3 84.0 - - - +
17H PRO* 1.3 67.6 - - + +
18H LEU* 4.4 0.9 - - - +
31H SER* 3.1 3.5 - - - -
32H PHE* 2.8 47.4 + - + +
34H VAL* 4.4 10.5 - - + -
303H THR* 3.4 33.2 - - + -
331H VAL* 4.2 22.4 - - + +
333H GLU 5.3 3.8 - - - +
335H ILE* 4.2 24.9 - - + +
364H LEU 4.6 2.9 - - - +
368H GLY* 3.9 18.8 - - - -
371H ARG* 4.3 4.7 - - - +
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Residues in contact with PRO 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU* 1.3 88.2 - - + +
18H LEU* 1.3 62.1 + - - +
30H GLU 3.6 9.2 - - - +
31H SER* 3.8 4.7 - - - -
331H VAL* 3.6 7.2 - - + +
332H GLN* 2.9 34.7 + - + +
333H GLU* 6.0 2.7 - - + +
371H ARG* 3.4 43.5 - - - +
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU 4.4 0.7 - - - +
17H PRO* 1.3 79.2 - - - +
19H LYS* 1.3 65.6 + - - +
20H GLN* 3.4 14.7 + - - +
22H TYR* 3.7 26.0 - - + -
29H ARG* 3.8 11.7 - - + +
30H GLU 2.9 14.3 + - - +
31H SER* 3.7 14.4 - - - +
32H PHE* 3.4 62.4 - - + +
330H LEU* 3.4 18.6 - - + +
331H VAL* 4.3 3.8 - - + -
332H GLN* 3.8 11.3 + - - +
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Residues in contact with LYS 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 1.3 73.2 - - - +
20H GLN* 1.3 69.4 + - + +
328H TRP* 5.9 4.3 - - - -
329H GLN* 3.1 33.7 + - - +
330H LEU* 2.9 13.4 + - - +
331H VAL 3.4 21.8 - - - +
332H GLN* 3.3 37.0 + - - +
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Residues in contact with GLN 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.2 19.2 - - - +
19H LYS* 1.3 87.5 - - + +
21H PRO* 1.3 84.6 - - + +
22H TYR* 3.3 2.4 + - - +
30H GLU* 5.6 1.1 - - - -
144H GLN* 3.5 42.3 + - - +
330H LEU* 4.8 1.5 + - + -
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Residues in contact with PRO 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLN* 1.3 96.2 - - + +
22H TYR* 1.3 60.7 + - - +
23H HIS* 3.7 20.7 + - + -
28H ILE* 3.2 24.7 - - + -
29H ARG 3.5 7.6 - - - +
30H GLU* 4.6 16.8 - - + +
144H GLN* 5.2 2.1 - - - +
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Residues in contact with TYR 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.7 16.8 - - + -
20H GLN 3.3 1.9 + - - +
21H PRO* 1.3 69.7 - - - +
23H HIS* 1.3 78.6 + - - +
24H TRP* 3.6 8.2 + - + -
28H ILE* 3.6 0.8 - - - -
29H ARG* 2.7 65.7 + - + +
32H PHE* 4.8 5.6 - + - -
142H PHE* 3.6 36.6 - + - -
144H GLN* 5.0 9.9 - - + -
169H LYS* 4.4 15.4 + - - -
301H PHE* 3.3 39.6 - + - -
327H MSE 4.5 0.2 - - - +
330H LEU* 4.3 14.8 - - + -
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Residues in contact with HIS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PRO* 3.7 27.9 + - + -
22H TYR* 1.3 86.3 - - - +
24H TRP* 1.3 60.7 - - - +
27H GLY 3.9 3.8 - - - +
28H ILE* 3.4 28.1 - - + +
146H GLU* 3.5 51.3 + - + +
169H LYS* 4.5 9.2 + - - -
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Residues in contact with TRP 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLN* 3.3 35.4 - - + -
90C GLU* 6.0 0.2 - - - -
93C GLY* 3.8 20.0 - - - +
94C HIS* 3.8 13.5 - + - -
22H TYR* 3.8 11.9 - - + -
23H HIS* 1.3 77.2 - - - +
25H SER* 1.3 69.6 + - - +
26H TYR* 3.1 52.1 + + + -
27H GLY 3.1 36.9 + - - +
28H ILE 3.6 22.5 + - - -
29H ARG* 3.3 42.5 - - + +
169H LYS* 5.6 3.4 - - - +
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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
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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