Contacts of the strand formed by residues 77 - 88 (chain B) in PDB entry 1CGP
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 GLU 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ARG* 5.2 4.9 - - - +
74B GLY 2.9 19.4 + - - +
75B LEU 3.5 1.6 + - - -
76B PHE* 1.3 76.3 - - + +
78B GLU* 1.3 103.2 + - - +
79B GLY 3.6 0.3 + - - -
80B GLN* 3.3 30.9 - - + +
99B TYR* 6.1 0.2 - - - -
103B ARG* 6.0 0.2 - - - +
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Residues in contact with GLU 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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75B LEU 5.4 0.3 - - - +
77B GLU* 1.3 103.0 + - - +
79B GLY* 1.3 62.5 + - - +
103B ARG* 3.1 32.1 + - - -
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Residues in contact with GLY 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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35B LYS* 5.5 6.5 - - - -
36B ALA 5.8 1.4 + - - -
77B GLU* 3.6 0.6 + - - -
78B GLU* 1.3 77.3 - - - +
80B GLN* 1.3 62.9 + - - +
81B GLU* 3.8 4.5 + - - +
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Residues in contact with GLN 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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122A ARG* 2.8 47.5 + - - +
125A GLN* 4.9 2.6 + - - -
35B LYS* 3.5 4.2 - - - +
36B ALA* 2.8 31.8 + - + +
73B LEU 2.8 20.6 + - - -
74B GLY* 3.9 14.8 + - - -
77B GLU* 3.3 38.1 - - + +
79B GLY* 1.3 78.1 - - - +
81B GLU* 1.3 66.6 + - - +
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Residues in contact with GLU 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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122A ARG* 5.8 0.7 + - - -
33B GLY* 2.9 28.9 - - - +
34B GLU 3.1 14.6 - - - +
35B LYS* 4.2 2.9 - - + +
36B ALA* 4.7 2.7 - - - +
73B LEU 5.9 0.2 - - - -
74B GLY* 5.6 0.7 - - - -
79B GLY 3.8 4.6 + - - +
80B GLN* 1.3 88.1 + - - +
82B ARG* 1.3 69.1 + - - +
83B SER* 3.4 4.2 + - - -
206B CMP 4.1 4.9 + - - -
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Residues in contact with ARG 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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30B ILE* 3.4 25.3 - - + +
31B HIS 3.3 16.6 - - - +
32B GLN* 3.3 5.7 - - - +
33B GLY* 2.9 23.4 + - - -
34B GLU* 2.9 31.7 + - - +
35B LYS 3.9 10.8 + - - +
36B ALA* 4.0 15.1 - - + +
37B GLU* 3.0 26.1 + - - -
38B THR 3.0 24.5 + - - -
40B TYR* 3.3 30.6 + - - -
71B GLY* 3.6 6.7 - - - -
81B GLU* 1.3 74.5 - - - +
83B SER* 1.3 59.6 + - - +
84B ALA 3.6 0.4 - - - -
206B CMP 3.3 32.4 + - - +
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Residues in contact with SER 83 (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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122A ARG* 6.0 0.4 - - - -
125A GLN* 4.9 14.6 - - - -
128A SER* 6.3 2.5 - - - -
32B GLN* 3.0 23.8 + - - -
51B ILE* 4.1 4.2 - - - +
73B LEU* 3.4 19.9 - - - +
81B GLU 3.4 3.6 + - - -
82B ARG* 1.3 71.6 - - - +
84B ALA* 1.3 60.8 + - - +
206B CMP 2.9 35.8 + - - -
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Residues in contact with ALA 84 (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 ILE* 3.5 17.3 - - - +
32B GLN* 3.4 22.1 + - - -
49B VAL* 3.8 25.4 - - + -
50B LEU 3.1 16.4 - - - +
51B ILE* 4.0 7.9 - - + -
61B LEU* 4.9 3.1 - - + -
82B ARG 3.6 0.6 + - - -
83B SER* 1.3 80.5 + - - +
85B TRP* 1.3 63.0 + - - +
206B CMP 3.6 13.6 - - + +
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Residues in contact with TRP 85 (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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28B THR* 4.2 16.2 - - + -
30B ILE 4.2 4.5 - - - +
31B HIS* 3.7 28.0 - + + +
32B GLN* 3.5 51.7 + - + +
49B VAL* 3.2 5.2 - - - +
50B LEU* 2.8 72.6 + - + +
51B ILE* 3.6 6.3 - - - -
52B LYS* 3.3 66.4 - - + +
84B ALA* 1.3 74.2 - - - +
86B VAL* 1.3 63.7 + - - +
87B ARG* 4.1 4.7 - - - +
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Residues in contact with VAL 86 (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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28B THR* 3.3 3.7 - - - -
29B LEU* 2.8 37.9 + - + -
30B ILE* 3.4 25.1 + - + +
47B VAL* 3.4 36.6 - - + -
48B ALA 3.3 4.3 - - - +
49B VAL* 3.9 8.7 - - + -
70B ILE* 3.8 35.0 - - + -
85B TRP* 1.3 79.0 - - - +
87B ARG* 1.3 53.4 + - - +
206B CMP 3.9 17.9 - - - +
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Residues in contact with ARG 87 (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 LYS* 3.5 31.9 - - - +
27B SER 3.1 5.6 - - - +
28B THR* 3.8 23.9 + - + +
47B VAL* 3.2 4.3 - - - +
48B ALA* 2.9 37.8 + - + +
50B LEU* 3.2 29.1 - - + +
58B GLU* 3.0 33.9 + - - -
85B TRP* 4.1 5.4 - - + +
86B VAL* 1.3 74.8 - - - +
88B ALA* 1.3 68.3 + - - +
89B LYS 3.6 0.2 + - - -
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Residues in contact with ALA 88 (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 TYR* 5.1 0.4 - - + -
24B PRO 3.5 20.0 - - - +
26B LYS* 2.8 27.0 + - - +
27B SER 2.7 15.3 + - - +
29B LEU* 4.0 14.5 - - + +
46B SER 4.0 0.4 - - - -
47B VAL* 3.9 7.8 - - + +
87B ARG* 1.3 75.7 - - - +
89B LYS* 1.3 60.5 + - - +
90B THR 3.4 17.0 - - - +
92B CYS* 4.4 8.1 - - + -
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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