Contacts of the strand formed by residues 6 - 24 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LYS* 1.3 72.4 - - - +
7D SER* 1.3 62.5 + - - +
8D ASN 3.9 13.2 - - - +
9D VAL* 4.4 2.9 - - + -
39D ILE* 3.7 21.3 - - + -
40D GLU 3.5 13.0 - - - +
41D ALA* 4.2 0.9 - - - +
42D ASP* 5.5 0.2 - - - -
71D LEU* 3.5 34.8 - - + +
72D VAL* 3.6 13.7 - - - +
73D GLY* 2.7 29.3 + - - -
74D HIS* 2.9 19.6 + - + +
75D SER 4.5 0.2 - - - +
76D PRO* 4.1 15.5 - - + -
113D MSE 3.8 31.9 - - + -
116D LEU* 4.7 2.0 - - + -
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Residues in contact with SER 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS 3.5 2.2 + - - -
6D ILE* 1.3 73.3 - - - +
8D ASN* 1.3 79.8 + - - +
40D GLU* 2.8 23.1 + - - +
41D ALA 3.4 13.2 + - - -
42D ASP* 3.8 19.9 - - - -
72D VAL* 3.5 14.1 - - - +
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Residues in contact with ASN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.6 3.5 - - - +
7D SER* 1.3 100.5 + - - +
9D VAL* 1.3 70.7 + - - +
10D ARG* 2.7 36.2 - - - +
40D GLU* 2.9 41.6 + - - +
72D VAL* 4.0 10.1 - - - -
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.4 3.8 - - + -
8D ASN* 1.3 84.3 - - - +
10D ARG* 1.3 69.3 + - - +
37D ILE* 4.3 2.2 - - + -
38D GLU 3.2 7.2 - - - +
39D ILE* 4.2 23.8 - - + -
65D TYR* 3.8 17.2 + - + -
68D ALA* 3.5 46.7 - - + +
69D LYS* 3.9 22.8 - - + +
71D LEU* 4.8 2.5 - - + -
72D VAL* 4.3 9.0 - - + -
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASN* 2.7 35.8 + - - +
9D VAL* 1.3 81.2 - - - +
11D VAL* 1.3 63.9 + - - +
12D ARG* 4.2 12.4 + - + +
36D LEU 3.7 0.5 - - - +
37D ILE* 3.4 5.9 - - - +
38D GLU* 2.8 66.6 + - + +
40D GLU* 3.1 24.1 + - - +
46D VAL* 4.0 19.6 - - - +
65D TYR* 4.8 2.5 - - - -
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG* 1.3 77.9 - - - +
12D ARG* 1.3 67.4 + - - +
13D PRO* 3.5 12.1 - - + +
35D ASN* 4.5 3.8 - - + -
36D LEU 3.2 8.5 - - - +
37D ILE* 4.4 6.7 - - + -
61D ALA* 4.0 30.5 - - + +
64D LEU* 3.8 21.8 - - + -
65D TYR* 3.5 48.0 - - + +
68D ALA* 5.3 0.2 - - + -
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Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 4.8 10.8 - - + +
11D VAL* 1.3 80.8 - - - +
13D PRO* 1.3 66.7 - - - +
14D LEU* 3.5 9.4 - - + +
35D ASN* 4.5 0.4 - - - -
36D LEU* 2.9 45.1 + - + +
38D GLU* 2.8 45.8 + - + -
360D LEU* 5.7 2.6 - - - +
362D GLU* 4.1 17.8 + - - -
365D VAL* 3.5 27.1 - - - +
366D ALA* 4.7 3.4 - - - +
369D GLU* 2.8 48.0 + - - +
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Residues in contact with PRO 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.5 11.0 - - + +
12D ARG* 1.3 83.7 - - - +
14D LEU* 1.3 66.3 + - - +
34D VAL 3.7 0.4 - - - +
35D ASN* 3.3 25.1 - - - +
57D GLN* 3.6 7.9 - - - +
61D ALA* 3.8 20.2 - - + -
369D GLU* 3.7 9.4 - - - +
372D TYR* 3.6 45.9 - - + +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.5 14.6 - - + +
13D PRO* 1.3 83.8 - - - +
15D VAL* 1.3 65.6 + - - +
16D LEU* 4.2 12.1 - - + -
33D ALA* 3.3 2.6 - - - -
34D VAL* 2.9 34.0 + - + +
36D LEU* 3.5 33.0 - - + -
57D GLN* 3.1 15.6 + - - +
335D ILE* 4.0 17.7 - - + -
365D VAL* 3.5 24.5 - - + +
368D GLY* 3.6 9.9 - - - -
369D GLU* 3.4 25.8 - - + +
372D TYR* 4.4 0.2 - - - -
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 1.3 79.4 - - - +
16D LEU* 1.3 64.2 + - - +
31D SER* 3.6 25.1 - - - +
32D PHE 3.6 5.2 - - - +
33D ALA* 4.5 4.0 - - + -
57D GLN* 3.8 15.3 - - - +
368D GLY* 3.2 8.1 + - - -
371D ARG* 3.2 45.6 + - + +
372D TYR* 3.6 22.2 - - - -
375D SER* 4.2 11.9 - - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.4 16.4 - - + -
15D VAL* 1.3 82.3 - - - +
17D PRO* 1.3 67.9 - - + +
18D LEU* 4.5 0.9 - - - +
31D SER* 3.0 4.0 - - - -
32D PHE* 2.8 45.9 + - + +
34D VAL* 4.7 4.7 - - + -
303D THR* 3.4 33.4 - - + -
331D VAL* 4.1 20.1 - - + +
333D GLU 4.9 5.6 - - - +
335D ILE* 4.2 28.3 - - + +
364D LEU* 4.4 4.3 - - + +
368D GLY* 4.0 17.5 - - - -
371D ARG* 4.0 6.3 - - - +
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Residues in contact with PRO 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 1.3 88.1 - - + +
18D LEU* 1.3 62.5 + - - +
30D GLU 3.6 9.9 - - - +
31D SER* 3.8 4.3 - - - -
331D VAL* 3.6 7.5 - - + +
332D GLN* 2.9 32.5 + - + +
333D GLU 4.4 0.8 + - - +
371D ARG* 3.3 46.7 - - - +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU 4.5 0.7 - - - +
17D PRO* 1.3 80.2 - - - +
19D LYS* 1.3 67.0 + - - +
20D GLN* 3.3 15.2 + - - +
22D TYR* 3.9 14.6 - - + -
29D ARG* 3.7 15.5 - - - +
30D GLU* 3.0 14.5 + - - +
31D SER* 3.4 23.8 - - - +
32D PHE* 3.5 59.5 - - + +
330D LEU* 3.4 19.1 - - + +
331D VAL* 4.4 2.9 - - + -
332D GLN* 3.9 7.0 - - - +
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 1.3 72.1 - - - +
20D GLN* 1.3 68.6 + - + +
328D TRP* 6.2 2.2 - - - -
329D GLN* 3.2 31.1 + - - +
330D LEU* 2.9 15.9 + - - +
331D VAL 3.6 10.8 - - - -
332D GLN* 3.1 43.9 - - - +
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.2 20.0 - - - +
19D LYS* 1.3 85.0 - - + +
21D PRO* 1.3 85.5 - - + +
22D TYR* 3.4 2.9 + - - +
30D GLU* 5.5 1.3 - - - -
144D GLN* 4.8 25.9 + - - +
330D LEU* 4.8 2.9 + - + -
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Residues in contact with PRO 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 1.3 99.0 - - + +
22D TYR* 1.3 61.3 + - - +
23D HIS* 3.7 20.7 + - + +
28D ILE* 3.2 26.5 - - + -
29D ARG 3.5 6.7 - - - +
30D GLU* 4.1 20.1 - - + +
144D GLN* 5.2 2.6 + - - -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 16.6 - - + -
20D GLN 3.4 2.5 + - - +
21D PRO* 1.3 70.5 - - - +
23D HIS* 1.3 78.5 + - - +
24D TRP* 3.7 4.1 + - + -
28D ILE* 3.5 1.2 - - - -
29D ARG* 2.7 66.4 + - + +
32D PHE* 4.8 5.6 - + - -
142D PHE* 3.5 29.4 - + - -
144D GLN* 3.6 28.7 - - - +
169D LYS* 5.0 11.3 - - - -
301D PHE* 3.4 38.7 - + - -
330D LEU* 4.3 12.6 - - + -
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Residues in contact with HIS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.7 23.2 + - + +
22D TYR* 1.3 85.7 - - - +
24D TRP* 1.3 61.6 + - - +
27D GLY 3.9 3.5 + - - +
28D ILE* 3.5 34.9 - - + +
144D GLN* 5.9 0.4 - - - +
145D GLY* 6.1 0.7 - - - -
146D GLU* 3.4 48.1 + - + +
169D LYS* 5.9 4.0 - - - +
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Residues in contact with TRP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 3.8 7.2 - - + -
23D HIS* 1.3 75.5 - - - +
25D SER* 1.3 79.2 + - - +
26D TYR* 2.9 41.6 + + + -
27D GLY 2.9 31.8 + - - +
28D ILE 3.7 20.2 + - - +
29D ARG* 3.7 42.4 - - - +
89E GLN* 3.4 31.6 - - + -
93E GLY* 3.7 32.1 - - - +
94E HIS* 3.8 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