Contacts of the strand formed by residues 6 - 23 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LYS* 1.3 72.9 - - - +
7C SER* 1.3 61.2 + - - +
8C ASN 3.9 9.9 - - - +
9C VAL* 4.4 5.2 - - + -
39C ILE* 3.7 20.9 - - + -
40C GLU 3.5 12.1 - - - +
41C ALA* 4.2 0.9 - - - +
71C LEU* 3.7 25.1 - - + +
72C VAL* 3.6 15.2 - - - +
73C GLY* 2.7 28.8 + - - -
74C HIS* 2.8 24.2 + - + +
76C PRO* 3.9 18.6 - - + -
113C MSE 3.7 36.6 - - + -
116C LEU* 4.6 2.0 - - + -
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS 3.5 1.0 + - - -
6C ILE* 1.3 74.5 - - - +
8C ASN* 1.3 83.4 + - - +
40C GLU* 2.7 19.7 + - - +
41C ALA 3.5 12.8 + - - -
42C ASP* 3.8 20.1 - - - -
72C VAL* 3.6 17.5 - - - +
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Residues in contact with ASN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.8 1.8 - - - +
7C SER* 1.3 110.1 + - - +
9C VAL* 1.3 71.9 + - - +
10C ARG* 3.9 20.4 - - + +
39C ILE* 3.7 0.2 - - - -
40C GLU* 2.8 44.3 + - + +
72C VAL* 4.5 4.5 - - - -
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.4 10.1 - - + -
8C ASN* 1.3 80.7 - - - +
10C ARG* 1.3 70.7 + - - +
37C ILE* 4.4 0.9 - - + -
38C GLU 3.2 11.0 - - - +
39C ILE* 4.5 10.5 - - + -
65C TYR* 3.9 19.0 + - + +
68C ALA* 3.4 33.2 - - + +
69C LYS* 4.0 35.0 - - + +
71C LEU* 4.6 2.0 - - + -
72C VAL* 4.2 13.8 - - + +
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Residues in contact with ARG 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASN* 3.9 20.3 - - + +
9C VAL* 1.3 79.5 - - - +
11C VAL* 1.3 64.2 + - - +
12C ARG* 4.2 7.6 - - + +
36C LEU 3.7 0.2 - - - +
37C ILE* 3.3 5.4 - - - +
38C GLU* 2.7 75.2 + - + +
40C GLU* 3.1 30.8 + - - +
46C VAL* 3.9 23.8 - - - +
65C TYR* 4.8 2.9 - - - -
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 1.3 76.7 - - - +
12C ARG* 1.3 67.7 + - - +
13C PRO* 3.7 10.7 - - + +
35C ASN* 4.4 4.0 - - + -
36C LEU 3.2 8.5 - - - +
37C ILE* 4.1 8.1 - - + -
61C ALA* 4.0 27.6 - - + +
64C LEU* 3.7 24.5 - - + -
65C TYR* 3.6 46.5 - - + +
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Residues in contact with ARG 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 4.8 5.6 - - + +
11C VAL* 1.3 80.9 - - - +
13C PRO* 1.3 67.7 - - - +
14C LEU* 3.4 10.5 + - + +
35C ASN* 4.5 0.4 - - - -
36C LEU* 3.0 41.5 + - + +
38C GLU* 2.9 43.9 + - - +
360C LEU* 5.7 2.8 - - - +
362C GLU* 4.4 17.8 + - - -
365C VAL* 3.3 26.3 - - - +
366C ALA* 4.6 2.8 - - - +
369C GLU* 2.9 48.7 + - + +
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Residues in contact with PRO 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 3.7 9.9 - - + +
12C ARG* 1.3 86.0 - - - +
14C LEU* 1.3 63.2 + - - +
35C ASN* 3.3 24.9 - - - +
57C GLN* 3.6 6.1 - - + +
61C ALA* 3.8 20.6 - - + -
369C GLU* 3.7 9.2 - - + +
372C TYR* 3.4 51.1 - - + +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 3.4 14.1 - - + +
13C PRO* 1.3 75.5 - - - +
15C VAL* 1.3 66.2 + - - +
16C LEU* 4.2 11.2 - - + -
33C ALA* 3.3 2.8 - - - -
34C VAL* 2.8 37.1 + - + +
36C LEU* 3.4 34.1 - - + -
57C GLN* 2.9 16.2 + - - +
335C ILE* 4.0 17.7 - - + -
365C VAL* 3.5 23.6 - - + +
368C GLY* 3.6 9.4 - - - -
369C GLU* 3.5 32.5 - - + +
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Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 1.3 78.7 - - - +
16C LEU* 1.3 65.2 + - - +
31C SER* 3.7 22.9 - - - +
32C PHE 3.6 6.1 - - - +
33C ALA* 4.4 5.4 - - + +
57C GLN* 3.8 15.0 - - - +
368C GLY* 3.2 5.6 + - - -
371C ARG* 3.1 50.1 + - + +
372C TYR* 3.7 22.0 - - + -
375C SER* 4.5 9.2 - - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.3 13.2 - - + -
15C VAL* 1.3 87.0 - - - +
17C PRO* 1.3 69.0 - - + +
18C LEU* 4.8 0.5 - - - +
31C SER* 2.9 3.7 - - - -
32C PHE* 2.8 47.2 + - + +
34C VAL* 4.6 4.5 - - + -
303C THR* 3.4 33.2 - - + -
331C VAL* 4.1 22.2 - - + +
333C GLU 5.3 4.3 - - - +
335C ILE* 4.0 28.5 - - + +
364C LEU 4.5 3.4 - - - +
368C GLY* 3.8 18.6 - - - -
371C ARG* 4.1 5.2 - - - +
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Residues in contact with PRO 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 1.3 88.5 - - + +
18C LEU* 1.3 64.6 - - - +
30C GLU 3.6 9.9 - - - +
31C SER* 3.6 4.7 - - - -
331C VAL* 3.6 7.0 - - + +
332C GLN* 2.9 36.7 + - + +
333C GLU* 5.5 5.4 - - + +
371C ARG* 3.5 40.4 - - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU 4.8 0.2 - - - +
17C PRO* 1.3 79.1 - - - +
19C LYS* 1.3 66.3 + - - +
20C GLN* 3.4 15.9 - - - +
22C TYR* 3.8 16.2 - - + -
29C ARG* 3.5 24.5 - - + +
30C GLU 2.9 14.5 + - - +
31C SER* 3.7 15.0 - - - +
32C PHE* 3.4 60.1 - - + +
330C LEU* 3.5 19.1 - - + +
331C VAL* 4.3 4.0 - - + -
332C GLN* 3.8 9.9 + - - +
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 1.3 72.3 - - - +
20C GLN* 1.3 65.9 + - + +
328C TRP* 6.0 4.1 - - - -
329C GLN* 3.0 32.7 + - - +
330C LEU* 2.8 18.8 + - - +
331C VAL 3.7 15.7 - - - +
332C GLN* 3.5 37.6 + - - +
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.4 19.8 - - - +
19C LYS* 1.3 80.7 - - + +
21C PRO* 1.3 85.7 + - + +
22C TYR* 3.4 2.8 + - - +
23C HIS* 6.0 1.4 - - - -
30C GLU* 5.5 0.9 - - - -
144C GLN* 3.5 43.6 - - - +
145C GLY* 5.0 3.6 - - - +
330C LEU* 4.7 4.0 + - + -
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Residues in contact with PRO 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 1.3 99.8 + - + +
22C TYR* 1.3 61.3 + - - +
23C HIS* 3.6 24.8 + - + +
28C ILE* 4.1 20.0 - - + -
29C ARG 3.4 7.2 - - - +
30C GLU* 3.1 29.5 - - - +
144C GLN* 5.3 1.0 + - - -
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.8 13.2 - - + -
20C GLN 3.4 1.7 + - - +
21C PRO* 1.3 71.0 - - - +
23C HIS* 1.3 76.0 + - - +
24C TRP* 3.6 6.1 - - + -
28C ILE* 3.3 2.8 - - - -
29C ARG* 2.6 71.1 + - + +
32C PHE* 4.9 4.0 - + - -
142C PHE* 3.6 35.9 - + - -
144C GLN* 4.3 19.1 - - - +
169C LYS* 5.4 10.1 + - + +
301C PHE* 3.4 37.9 - + - -
327C MSE 4.6 0.3 - - - +
330C LEU* 4.3 13.9 - - + -
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Residues in contact with HIS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 6.0 1.6 - - - -
21C PRO* 3.6 25.4 + - + +
22C TYR* 1.3 84.8 - - - +
24C TRP* 1.3 62.3 + - - +
27C GLY 3.9 4.4 + - - +
28C ILE* 3.1 26.9 - - + +
146C GLU* 3.5 50.4 + - + +
169C LYS* 4.0 12.1 + - - -
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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