Contacts of the strand formed by residues 14 - 21 (chain B) in PDB entry 2G1Y
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 GLN 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR 3.6 1.2 - - - +
10B TYR* 2.8 59.5 + - + +
12B ASP 3.6 0.8 - - - -
13B THR* 1.3 83.5 + - - +
15B TYR* 1.3 65.5 + - - +
16B TYR* 3.9 13.2 - - + -
116B LEU* 3.4 19.6 + - - +
117B ALA* 3.5 1.7 - - - -
118B GLU* 2.7 33.1 + - - +
119B PHE* 3.6 6.8 - - + -
886B 5IG 3.0 48.3 + - + +
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Residues in contact with TYR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.7 5.4 - - + -
8B THR 3.4 5.4 - - - -
9B ASN* 3.2 22.6 + - + -
12B ASP* 3.4 25.2 + - - -
14B GLN* 1.3 77.4 - - - +
16B TYR* 1.3 64.7 + - - +
31B VAL* 3.3 25.6 - - - +
32B PHE 4.6 0.7 + - - -
157B TYR* 3.4 64.6 + + + -
158B ASN 2.5 23.1 + - - -
168B GLY 3.4 27.1 - - - -
169B GLY* 4.9 0.9 - - - -
312B ALA* 3.9 9.2 - - + -
316B ARG* 3.1 22.5 + - - -
886B 5IG 3.2 11.2 + - - -
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Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 10.1 - - - +
8B THR* 2.7 64.7 + - + +
10B TYR* 3.5 28.4 - - + +
14B GLN* 3.9 11.2 - - + -
15B TYR* 1.3 83.2 - - - +
17B GLY* 1.3 55.6 + - - +
29B LYS* 4.1 34.1 - - + -
30B VAL 3.0 26.0 - - - +
31B VAL* 4.1 0.9 - - - +
32B PHE* 5.4 0.2 - - - -
118B GLU* 3.3 34.2 + - + +
119B PHE* 3.9 19.5 - + + -
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.0 4.7 - - - -
6B ILE 3.7 16.6 - - - -
7B LEU* 3.6 11.1 - - - +
8B THR* 5.8 0.4 - - - -
16B TYR* 1.3 75.2 - - - +
18B GLU* 1.3 66.5 + - - -
28B PHE 3.4 0.2 - - - +
29B LYS* 3.3 4.9 - - - -
30B VAL* 2.7 34.5 + - - +
32B PHE* 4.1 3.1 - - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.0 19.1 - - - +
6B ILE 4.6 5.8 + - - +
8B THR* 5.5 3.1 + - - -
17B GLY* 1.3 75.6 - - - +
19B ILE* 1.3 70.3 + - - +
27B THR* 3.8 24.2 - - + +
28B PHE 3.2 8.7 - - - +
29B LYS* 4.9 11.7 - - + -
93B THR 4.6 1.2 - - - +
94B VAL* 5.1 0.2 - - - -
95B GLY* 4.8 6.2 + - - -
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Residues in contact with ILE 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 GLU* 1.3 79.9 - - - +
20B GLY* 1.3 60.7 + - - +
21B ILE* 4.2 18.8 - - + -
26B GLN 3.7 0.7 - - - +
27B THR* 3.6 4.9 - - - +
28B PHE* 3.1 28.3 + - + +
30B VAL* 3.6 42.0 - - + -
32B PHE* 3.7 17.5 - - + -
39B VAL* 4.9 3.6 - - + -
41B VAL* 5.0 1.3 - - + -
92B ILE* 4.1 23.3 - - + -
93B THR 3.1 13.9 - - - +
94B VAL* 4.6 10.1 - - + -
123B VAL* 3.9 15.0 - - + -
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Residues in contact with GLY 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 ILE* 1.3 73.4 - - - +
21B ILE* 1.3 64.1 + - - -
22B GLY 4.3 0.4 - - - -
25B PRO* 4.3 10.1 - - - -
26B GLN 3.5 9.6 - - - -
27B THR* 4.7 1.8 - - - -
91B ILE 3.7 0.2 - - - +
92B ILE* 3.0 9.5 - - - +
93B THR* 2.5 53.0 + - - -
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Residues in contact with ILE 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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19B ILE* 4.2 13.0 - - + -
20B GLY* 1.3 78.8 - - - +
22B GLY* 1.3 65.1 + - - +
26B GLN* 2.9 35.6 + - - +
28B PHE* 3.7 32.3 - - + -
39B VAL* 5.6 1.1 - - + -
41B VAL* 3.8 28.3 - - + -
59B PHE* 3.5 21.9 - - + -
90B ASP* 4.1 4.9 - - + -
91B ILE 3.5 4.0 - - - +
92B ILE* 4.1 15.3 - - + -
103B PHE* 3.6 30.7 - - + -
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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