Contacts of the strand formed by residues 11 - 20 (chain B) in PDB entry 3QG2
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.4 9.9 - - + -
6B CYS* 3.1 9.6 + - - -
9B PHE* 4.2 16.6 - - + +
10B ASP* 1.3 72.6 - - - +
12B TYR* 1.3 62.4 + - - +
149B LEU* 5.0 6.1 - - + -
150B ILE* 4.0 27.1 - - + -
153B LEU* 4.5 5.8 - - + -
161B CYS* 3.5 13.5 - - + +
163B ILE* 3.8 31.2 - - + -
173B PHE* 4.7 5.6 - - + -
178B LEU* 3.1 33.3 - - + +
179B ILE* 3.7 4.6 - - + -
180B LYS* 2.9 29.7 + - - +
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Residues in contact with TYR 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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285A GLU* 2.8 31.0 + - - +
10B ASP* 3.9 13.6 + - + -
11B ILE* 1.3 75.9 - - - +
13B ALA* 1.3 56.4 + - - +
160B LYS* 3.3 36.2 + - + -
161B CYS 2.7 11.7 + - - +
162B PHE* 3.3 32.6 - + + -
163B ILE* 2.7 35.2 + - - +
179B ILE* 4.3 3.1 - - - -
180B LYS* 2.8 35.8 + - + -
181B LYS* 3.3 45.5 - - + +
183B TYR* 4.0 14.4 - + + -
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Residues in contact with ALA 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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12B TYR* 1.3 75.0 - - - +
14B ILE* 1.3 54.9 + - - +
163B ILE* 3.6 11.2 - - + +
170B TYR* 4.5 14.6 - - + -
174B LEU* 5.5 1.6 - - + -
179B ILE* 3.8 26.0 - - + +
181B LYS 2.9 11.9 + - - +
182B ILE* 3.1 15.5 - - + -
183B TYR* 2.7 34.5 + - - -
197B PHE* 5.4 2.5 - - + -
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Residues in contact with ILE 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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13B ALA* 1.3 75.2 - - - +
15B CYS* 1.3 59.0 + - - +
57B TYR* 4.6 7.0 - - + -
58B PHE* 3.8 30.5 - - + -
61B VAL* 4.1 27.8 - - + -
62B THR* 4.4 6.3 - - + -
162B PHE* 4.5 11.7 - - + -
163B ILE 3.1 6.7 + - - +
164B LEU* 3.6 31.0 - - + -
170B TYR* 2.7 23.1 + - - -
183B TYR* 3.2 24.2 - - + +
709B CP6 2.8 24.0 + - - +
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Residues in contact with CYS 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 ILE* 1.3 75.8 - - - +
16B ALA* 1.3 54.0 + - - +
17B CYS* 4.1 2.9 - - - -
40B LEU* 4.3 2.2 - - + -
170B TYR* 3.3 21.8 - - + +
182B ILE* 4.3 4.3 - - - -
183B TYR 2.8 10.3 + - - +
184B PHE* 3.5 34.3 - - - -
185B THR 2.8 27.5 + - - -
197B PHE* 3.4 31.0 - - + -
709B CP6 3.1 19.4 + - - -
710B NDP 3.4 5.6 - - - +
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Residues in contact with ALA 16 (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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15B CYS* 1.3 74.2 - - - +
17B CYS* 1.3 64.7 + - - +
39B GLY 3.5 2.8 - - - +
48B TRP* 3.4 16.8 - - + -
54B ASP* 3.5 28.5 - - - +
185B THR* 3.5 12.3 - - + -
187B ILE* 4.6 1.6 - - + -
709B CP6 3.6 11.2 - - + +
710B NDP 2.6 41.1 + - - +
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Residues in contact with CYS 17 (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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15B CYS* 4.1 4.3 - - - -
16B ALA* 1.3 78.9 - - - +
18B CYS* 1.3 60.3 + - - +
37B PHE* 3.5 20.0 - - - +
38B ARG* 3.7 4.0 - - - +
39B GLY 3.1 5.2 - - - +
40B LEU* 3.6 24.2 - - - -
48B TRP* 4.3 0.2 - - - -
184B PHE* 3.4 35.2 - - + -
185B THR 2.9 9.7 + - - +
186B ARG* 3.9 0.2 - - - -
187B ILE* 3.0 26.6 + - - +
197B PHE* 3.7 19.3 - - - -
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Residues in contact with CYS 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 CYS* 1.3 73.0 - - - +
19B LYS* 1.3 68.0 + - - +
37B PHE* 4.3 1.6 - - - -
38B ARG 3.1 9.4 + - - -
39B GLY* 2.8 31.7 + - - -
47B PRO* 3.8 2.9 - - - -
48B TRP* 3.5 23.5 - - + -
187B ILE* 3.4 12.3 - - + -
189B SER 3.5 3.1 - - - +
191B TYR* 3.5 29.4 - - + -
193B CYS* 3.5 32.5 - - - -
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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 CYS* 1.3 83.1 - - - +
20B VAL* 1.3 62.3 + - - +
27B LYS 5.4 5.9 + - - -
29B ASN* 5.6 3.7 + - - +
32B PHE* 5.2 5.4 - - + -
36B THR* 3.6 36.6 - - + +
37B PHE* 3.8 13.7 - - + -
187B ILE 4.4 0.4 - - - +
188B ASN* 3.1 24.9 + - - +
189B SER 3.0 20.9 + - - +
190B THR* 3.3 13.6 + - - +
191B TYR 3.2 23.7 + - - +
595B ASN* 2.8 39.9 + - - +
597B VAL* 3.8 11.9 - - + +
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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
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19B LYS* 1.3 79.7 - - - +
21B GLU* 1.3 76.9 + - + +
22B SER* 4.1 4.8 + - - +
29B ASN* 5.3 6.6 + - - -
36B THR 4.3 3.2 + - - -
38B ARG* 4.1 25.7 + - + +
39B GLY* 4.0 18.4 - - - +
190B THR* 3.5 6.6 + - - +
191B TYR 4.0 6.5 - - - +
193B CYS* 4.3 11.4 - - + +
196B PHE* 3.5 42.4 - - + -
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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
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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