Contacts of the strand formed by residues 26 - 33 (chain B) in PDB entry 2GYR
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 LEU 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.3 32.8 - - + +
12B VAL* 3.3 27.6 - - - +
13B PRO* 3.6 16.6 - - + -
25B GLU* 1.3 80.7 - - - +
27B VAL* 1.3 63.0 - - - +
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Residues in contact with VAL 27 (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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11B LEU* 3.7 5.6 - - - -
12B VAL* 2.8 39.6 + - + +
14B VAL* 3.7 20.6 - - + -
17B LEU* 4.0 18.8 - - + -
25B GLU* 3.9 7.0 - - + +
26B LEU* 1.3 80.3 - - - +
28B ARG* 1.3 67.0 + - - +
29B PHE 3.5 0.3 + - - -
78B VAL* 3.7 25.6 - - + -
79B SER 3.7 21.5 - - - +
80B PHE* 4.0 5.4 - - + -
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Residues in contact with ARG 28 (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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9B SER* 2.9 44.0 + - - +
10B GLN* 3.4 11.7 - - - +
11B LEU* 3.3 36.2 - - - +
27B VAL* 1.3 82.1 - - - +
29B PHE* 1.3 59.7 + - - +
30B ARG* 4.1 31.8 - - - +
78B VAL* 4.1 14.7 - - - +
94B SER* 4.6 2.5 + - - -
52C GLY 3.7 19.8 + - - -
53C ALA* 4.8 3.4 + - - +
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Residues in contact with PHE 29 (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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43A HIS* 3.9 17.3 - + - -
46A SER* 3.9 17.9 - - - -
47A LEU* 3.9 23.6 - - + -
50A LEU* 3.5 24.5 - - + -
56A LEU* 4.7 3.8 - - + -
8B ARG 3.8 1.2 - - - +
10B GLN* 3.0 27.8 + - - +
12B VAL* 3.8 21.5 - - + -
17B LEU* 3.8 17.9 - - + -
28B ARG* 1.3 76.4 - - - +
30B ARG* 1.3 62.3 - - - +
31B PHE* 4.0 32.8 - + + -
78B VAL* 4.9 4.7 - - + -
93B LEU* 3.4 22.4 - - + -
94B SER* 3.9 7.2 - - - -
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Residues in contact with ARG 30 (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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43A HIS* 3.5 6.1 + - - -
7B LEU* 3.9 20.4 - - + -
8B ARG 2.8 9.6 - - - +
9B SER* 3.2 33.2 + - - +
28B ARG* 4.1 31.1 - - - +
29B PHE* 1.3 81.1 - - - +
31B PHE* 1.3 61.4 + - - +
76B GLU* 3.3 24.8 + - - -
94B SER* 3.0 8.9 + - - +
95B ALA* 3.0 44.0 + - - +
96B THR* 5.7 0.2 - - - +
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Residues in contact with PHE 31 (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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43A HIS* 4.2 8.5 - - + +
47A LEU* 4.3 13.5 - - + -
56A LEU* 3.5 29.4 - - + -
57A ARG 4.7 0.7 - - - -
59A PRO* 3.9 22.4 - - + -
64A PRO* 3.9 29.2 - - + -
7B LEU* 3.4 6.9 - - - +
8B ARG* 2.4 80.8 + - + +
9B SER 4.8 0.4 - - - -
10B GLN* 3.9 19.7 - - - -
29B PHE* 4.0 26.5 - + + -
30B ARG* 1.3 77.7 - - - +
32B CYS* 1.3 61.9 + - - +
33B SER* 4.3 0.2 - - - -
95B ALA* 4.0 7.0 - - - -
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Residues in contact with CYS 32 (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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43A HIS* 5.2 1.4 - - - -
47A LEU* 5.4 2.1 - - - +
64A PRO* 3.6 15.8 - - - +
65A VAL 4.8 2.8 + - - +
6B ARG 3.7 0.4 - - - -
7B LEU* 4.3 2.5 - - - -
31B PHE* 1.3 76.6 - - - +
33B SER* 1.3 66.3 + - - +
70B CYS* 3.8 10.8 - - - +
71B ARG* 3.8 15.9 - - - +
72B PRO* 3.4 30.1 - - + +
95B ALA* 4.3 1.1 - - - +
97B ALA 3.6 2.0 - - - -
98B CYS* 2.0 58.1 - - + -
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Residues in contact with SER 33 (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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59A PRO* 3.3 17.1 - - - +
60A PRO 5.0 0.2 + - - -
62A SER 4.0 4.2 + - - -
64A PRO* 3.8 25.6 - - - -
4B GLY 3.1 2.8 - - - +
6B ARG 2.9 28.4 + - - +
8B ARG* 2.8 40.3 + - - +
32B CYS* 1.3 80.0 - - - +
34B GLY* 1.3 59.4 + - - +
70B CYS* 3.4 12.2 - - - -
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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