Contacts of the strand formed by residues 75 - 82 (chain B) in PDB entry 1C1D
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 GLY 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 3.2 18.8 - - - -
32B THR* 4.4 0.9 - - - -
34B LEU* 4.7 4.5 - - - -
35B GLY 3.3 11.5 + - - -
36B PRO 2.8 14.2 + - - +
37B ALA* 3.6 4.9 - - - -
38B ALA* 3.1 14.2 + - - +
64B THR* 4.5 4.0 - - - -
67B MET* 3.6 14.0 - - - +
74B MET* 1.4 78.9 - - - +
76B GLY* 1.4 58.8 + - - -
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Residues in contact with GLY 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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30B ASP* 2.8 29.6 + - - +
31B SER 2.9 14.1 + - - -
37B ALA* 3.5 8.4 - - - +
38B ALA 3.7 3.6 - - - -
60B ALA 3.8 6.5 - - - -
63B MET* 3.8 2.0 - - - -
64B THR* 3.3 32.5 + - - +
75B GLY* 1.4 75.3 - - - -
77B GLY* 1.3 52.5 + - - -
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 3.0 14.8 - - - -
37B ALA* 4.1 10.5 - - - -
38B ALA 3.1 10.5 + - - +
39B GLY* 3.1 22.4 - - - -
60B ALA* 3.8 7.2 - - - -
63B MET* 3.3 10.9 - - - +
76B GLY* 1.3 74.7 - - - -
78B LYS* 1.3 62.5 + - - +
113B TYR* 4.1 5.8 - - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL 4.0 0.3 - - - +
27B ILE* 3.5 2.1 - - - +
28B ARG* 2.8 33.0 + - - +
39B GLY 4.4 0.2 - - - -
40B GLY 3.4 21.7 - - - +
42B ARG* 4.9 1.8 - - - -
56B ALA* 3.9 10.8 - - - +
59B LEU* 3.6 35.5 + - + +
60B ALA 3.8 15.3 - - - +
63B MET* 4.3 10.2 - - + -
77B GLY* 1.3 77.0 - - - +
79B SER* 1.3 71.7 + - - +
80B VAL* 4.9 0.9 - - + -
113B TYR* 3.8 7.7 - - - -
118B ASP* 3.1 39.4 + - - -
262B ASN* 4.1 7.1 - - - +
761B PHE* 3.4 23.0 + - - -
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Residues in contact with SER 79 (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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26B VAL 3.2 8.3 - - - -
27B ILE* 3.6 5.5 - - - +
40B GLY 2.9 8.1 + - - +
41B THR* 3.7 12.8 - - - -
42B ARG* 2.9 26.4 + - - +
78B LYS* 1.3 76.2 - - - +
80B VAL* 1.4 66.4 + - - +
102B HIS* 3.2 34.3 - - - -
113B TYR* 2.8 29.3 + - - -
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Residues in contact with VAL 80 (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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25B PHE* 3.8 0.9 - - - -
26B VAL* 2.8 37.8 + - + +
42B ARG* 3.3 8.5 - - + +
46B TYR* 3.4 42.8 - - + +
52B ALA* 4.0 16.8 - - + +
55B ASP 4.6 0.4 - - - -
56B ALA* 3.7 37.2 - - + +
59B LEU* 4.4 13.7 - - + -
78B LYS* 4.9 0.7 - - + -
79B SER* 1.4 76.2 - - - +
81B ILE* 1.3 65.6 + - - +
82B ALA 3.9 0.9 + - - -
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Residues in contact with ILE 81 (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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23B ALA* 4.5 5.2 - - + -
24B HIS 3.5 10.1 - - - +
25B PHE* 4.1 15.9 - - + +
41B THR* 3.8 26.5 - - + -
42B ARG 2.8 12.4 + - - +
43B ALA* 3.4 10.4 - - + -
44B ALA 3.0 27.5 + - - +
80B VAL* 1.3 76.1 - - - +
82B ALA* 1.3 61.1 + - - +
83B LEU* 3.4 16.7 + - + +
95B TRP* 5.2 1.6 - - + -
98B ILE* 3.8 34.5 - - + -
99B LEU* 4.9 7.6 - - + -
102B HIS* 4.1 24.7 - - + +
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Residues in contact with ALA 82 (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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22B GLY 4.4 0.9 - - - +
23B ALA* 3.6 4.9 - - - +
24B HIS* 2.9 48.3 + - + +
26B VAL* 6.1 0.9 - - + -
44B ALA 3.4 6.3 - - - -
46B TYR* 4.0 21.1 - - + +
49B LEU* 4.5 7.4 - - + -
52B ALA* 4.2 15.5 - - + -
80B VAL 3.9 1.8 - - - +
81B ILE* 1.3 69.2 - - - +
83B LEU* 1.3 66.1 + - - +
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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