Contacts of the strand formed by residues 52 - 57 (chain B) in PDB entry 1I7H
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 HIS 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 5.4 2.8 - - - +
49B THR* 3.1 21.0 + - - +
50B THR 3.2 3.5 - - - +
51B CYS* 1.3 80.5 - - - +
53B CYS* 1.3 84.7 + - - +
54B ILE* 4.2 3.8 - - + +
73B LEU* 4.5 6.7 - - + -
76B ALA* 3.9 16.2 - - + +
77B TRP 3.3 27.1 + - - -
78B GLY 3.4 17.7 - - - -
79B LEU* 4.1 2.9 - - - -
83B SER* 2.7 32.0 + - - -
84B ARG 3.6 10.3 - - - -
85B LEU* 4.5 4.9 - - + +
100B ILE* 4.9 1.6 - - - +
101B PRO* 3.0 37.2 - - + +
104B THR* 4.6 6.3 - - + +
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Residues in contact with CYS 53 (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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27B ILE* 4.2 17.5 - - + -
38B ILE* 5.7 3.6 - - + -
51B CYS 4.1 3.4 - - - +
52B HIS* 1.3 78.7 - - - +
54B ILE* 1.3 64.3 + - - +
55B VAL* 4.4 7.6 - - - -
83B SER* 3.3 4.3 - - - -
84B ARG* 2.8 41.6 + - - -
86B SER* 3.9 22.2 - - - -
98B VAL* 3.7 27.4 - - + -
99B GLU 3.5 8.1 - - - +
100B ILE* 5.0 3.6 - - + -
101B PRO* 3.9 4.0 - - + -
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Residues in contact with ILE 54 (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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52B HIS* 4.2 3.8 - - + +
53B CYS* 1.3 78.3 - - - +
55B VAL* 1.3 62.1 + - - +
56B ARG* 3.2 41.4 + - - +
78B GLY 4.2 12.6 - - - +
80B GLU* 3.3 29.6 - - + +
82B GLU* 3.7 20.0 - - + +
83B SER* 4.0 13.2 - - - +
98B VAL* 3.4 1.6 - - - -
99B GLU* 2.7 56.2 + - + +
101B PRO* 4.8 13.2 - - + -
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Residues in contact with VAL 55 (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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27B ILE* 4.1 15.9 - - + -
53B CYS* 4.4 4.3 - - - -
54B ILE* 1.3 68.6 - - - +
56B ARG* 1.3 62.1 + - - +
57B GLU 3.4 22.1 + - - +
58B GLY 3.9 3.1 - - - -
59B PHE* 3.7 25.0 - - + +
62B LEU* 3.8 24.0 - - + -
82B GLU* 3.0 39.8 + - - +
84B ARG* 4.1 14.4 - - + -
96B LEU* 4.2 10.8 - - + -
97B VAL 3.6 6.1 - - - +
98B VAL* 4.5 5.2 - - + +
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Residues in contact with ARG 56 (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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7B LEU* 4.1 20.6 - - + -
54B ILE* 3.2 24.5 + - - +
55B VAL* 1.3 72.3 - - - +
57B GLU* 1.3 77.2 + - + +
80B GLU* 2.6 43.9 + - - -
82B GLU* 3.9 23.1 + - - +
97B VAL* 2.9 22.5 + - + +
99B GLU* 3.1 36.5 + - + -
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Residues in contact with GLU 57 (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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77A TRP* 3.9 13.2 - - + -
102A ARG* 3.1 61.5 + - + +
103A TYR* 4.6 7.0 - - + -
55B VAL* 3.2 8.0 - - - +
56B ARG* 1.3 95.2 - - + +
58B GLY* 1.3 59.3 + - - +
59B PHE 3.5 2.2 - - - +
82B GLU* 5.4 1.1 - - - -
95B ASP 4.6 0.9 - - - -
96B LEU* 3.4 7.1 - - - -
97B VAL* 3.2 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