Contacts of the strand formed by residues 46 - 50 (chain B) in PDB entry 2GBR
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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.4 5.1 - - + +
27B LYS* 3.0 29.0 + - - +
31B GLN* 4.4 10.9 - - - +
34B GLU* 4.7 5.4 + - - +
38B ALA* 4.5 3.8 + - - +
41B ILE* 3.2 49.0 + - + +
42B PRO 3.5 5.5 + - - +
43B PRO* 3.4 15.3 - - - +
44B ASP 3.2 3.8 + - - +
45B GLN* 1.3 77.9 - - - +
47B ARG* 1.3 65.0 + - - +
57B ASP* 4.8 0.7 - - - +
74B LEU* 3.2 37.3 - - + +
75B VAL 3.4 9.6 - - - +
76B LEU* 4.9 2.7 - - + -
77B ARG* 4.2 7.2 + - - +
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Residues in contact with ARG 47 (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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9A THR* 4.9 7.1 + - - -
11A LYS* 4.6 5.1 - - - +
27B LYS* 5.2 0.7 - - - +
46B GLN* 1.3 72.9 - - - +
48B LEU* 1.3 63.4 + - - +
49B ILE* 4.5 3.1 - - + +
54B GLN* 2.7 63.6 + - - +
55B LEU 4.7 9.6 - - - +
57B ASP* 5.8 1.8 - - - -
73B HIS 3.6 0.3 - - - +
74B LEU* 3.5 6.3 - - - +
75B VAL* 2.8 47.8 + - + +
76B LEU 5.0 0.8 + - - -
77B ARG* 3.3 68.2 - - + +
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Residues in contact with LEU 48 (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 8.7 - - + -
23B ILE* 3.7 21.0 - - + +
26B VAL* 3.9 22.7 - - + -
27B LYS* 3.7 27.9 - - + +
30B ILE* 3.9 19.3 - - + -
47B ARG* 1.3 74.5 - - - +
49B ILE* 1.3 63.1 + - - +
54B GLN* 4.0 0.2 - - - -
55B LEU* 3.0 46.4 + - + +
57B ASP* 5.9 0.4 + - - -
72B LEU* 3.8 29.6 - - + -
73B HIS 3.4 10.5 - - - +
74B LEU* 4.0 10.5 - - + +
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Residues in contact with ILE 49 (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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9A THR 5.4 1.8 - - - +
10A GLY* 5.1 9.4 - - - +
47B ARG* 4.5 4.9 - - - -
48B LEU* 1.3 84.0 - - - +
50B PHE* 1.3 63.5 + - - +
52B GLY* 4.1 12.6 - - - +
53B LYS 3.2 19.3 - - - +
54B GLN* 3.5 34.8 - - + +
55B LEU* 4.3 2.0 - - - -
72B LEU* 3.4 6.4 - - - -
73B HIS* 2.9 43.6 + - + +
75B VAL* 3.8 31.4 - - + -
311B CD 4.2 14.1 - - - -
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Residues in contact with PHE 50 (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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49B ILE* 1.3 76.9 - - - +
51B ALA* 1.3 86.5 + - + +
52B GLY 3.3 0.7 - - - -
53B LYS* 2.8 43.2 + - - +
55B LEU* 3.9 19.0 - - + +
64B TYR* 4.0 13.7 - - + -
65B ASN 4.5 4.5 - - - -
66B ILE* 3.4 33.4 - - + -
67B GLN 5.3 0.2 - - - -
70B SER* 3.7 30.5 - - - -
71B THR 3.6 21.3 - - - -
72B LEU* 4.3 4.7 - - + -
73B HIS* 5.8 1.1 - - - -
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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