Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 2GBK
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 THR 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.5 18.9 - - - +
6B LYS* 3.6 35.8 + - + +
51B ILE 4.6 1.2 - - - +
52B PHE* 3.5 18.8 - - - -
53B ALA 5.5 0.2 + - - -
71B GLU 3.9 2.7 + - - -
72B SER* 1.3 74.4 - - - +
74B LEU* 1.3 74.9 + - - +
75B HIS* 4.0 15.6 + - - +
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Residues in contact with LEU 74 (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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3B ILE* 4.4 21.1 - - + -
4B PHE 2.9 14.8 + - - +
5B VAL* 3.3 8.2 - - + -
6B LYS 3.0 23.6 + - - -
33B VAL* 4.7 3.4 - - + -
50B LEU* 4.1 28.9 - - + -
51B ILE 3.5 11.2 - - - +
52B PHE* 4.1 11.4 - - + -
57B LEU* 3.9 26.2 - - + -
63B LEU* 4.7 5.4 - - + -
68B ILE* 4.0 30.5 - - + -
72B SER 4.4 3.8 - - - +
73B THR* 1.3 85.4 - - - +
75B HIS* 1.3 63.0 + - - +
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Residues in contact with HIS 75 (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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6B LYS* 3.1 29.4 + - + +
7B THR 3.3 27.0 + - - -
8B LEU* 4.2 22.1 - - + -
9B THR* 5.0 3.4 - - - -
12B ARG* 3.8 7.6 - - - -
49B ARG 3.6 0.3 - - - +
50B LEU* 3.4 7.1 - - - -
51B ILE* 2.9 56.4 + - + +
73B THR* 4.0 15.9 - - + +
74B LEU* 1.3 76.9 - - - +
76B LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 76 (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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5B VAL* 3.8 18.6 - - + -
6B LYS 2.7 12.7 + - - +
7B THR* 3.6 24.4 - - + +
8B LEU 4.4 0.2 + - - -
37B ILE* 3.9 29.2 - - + -
43B ILE* 4.0 20.6 - - + -
48B GLN* 3.8 26.9 - - + +
49B ARG 3.6 14.8 - - - +
50B LEU* 4.0 12.1 - - + -
75B HIS* 1.3 72.7 - - - +
77B VAL* 1.3 77.0 + - - +
78D LEU* 4.1 12.9 - - + +
80D LEU* 4.5 11.2 - - + -
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Residues in contact with VAL 77 (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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8B LEU* 3.8 37.2 - - + +
47B GLN 3.7 2.6 - - - +
48B GLN* 4.0 0.2 - - - -
49B ARG* 3.1 46.4 + - + +
51B ILE* 5.3 5.8 - - + -
75B HIS 5.2 1.3 - - - -
76B LEU* 1.3 84.5 - - - +
78B LEU* 1.3 62.1 + - - +
11D VAL* 3.8 26.0 - - + -
14D LEU* 5.0 9.0 - - + -
15D VAL* 4.0 15.9 - - + -
78D LEU* 4.2 7.8 - - - +
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Residues in contact with LEU 78 (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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43B ILE* 4.2 12.8 - - + -
47B GLN* 3.5 15.3 - - + +
49B ARG* 5.1 0.2 - - - -
77B VAL* 1.3 75.8 - - - +
79B ARG* 1.3 60.4 + - - +
80B LEU* 4.0 3.6 - - + -
7D THR* 4.0 23.6 + - + +
11D VAL* 3.3 22.4 - - - +
15D VAL* 3.6 7.0 - - - +
16D GLY 4.7 0.7 - - - +
43D ILE* 4.2 22.4 - - + -
76D LEU* 4.2 32.3 - - + +
77D VAL* 4.5 1.8 - - - -
78D LEU* 3.6 49.8 - - + +
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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