Contacts of the strand formed by residues 77 - 88 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLY 3.1 12.3 + - - +
75A LEU 5.4 0.2 - - - -
76A PHE* 1.3 79.9 - - + +
78A GLU* 1.3 109.0 + - - +
79A GLY 3.2 1.9 + - - -
80A GLN* 3.1 46.2 + - - +
103A ARG* 6.0 0.7 - - - -
122B ARG* 4.8 6.1 - - - +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 5.8 0.3 - - - +
76A PHE 4.2 0.4 + - - -
77A GLU* 1.3 102.1 + - - +
79A GLY* 1.3 62.5 + - - +
99A TYR* 6.0 0.3 - - - -
100A LYS* 5.3 2.3 - - - +
103A ARG* 3.4 30.2 + - - +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 6.1 2.7 - - - -
36A ALA 5.6 3.9 + - - -
37A GLU* 6.1 1.6 - - - -
77A GLU* 3.2 1.8 + - - -
78A GLU* 1.3 78.9 + - - +
80A GLN* 1.3 63.2 + - - +
81A GLU* 4.2 2.1 + - - +
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.7 3.7 - - - +
36A ALA* 2.9 32.2 + - - +
73A LEU 3.4 21.7 + - - +
74A GLY* 4.1 9.1 - - - -
76A PHE* 5.6 0.6 - - - +
77A GLU* 3.1 53.6 + - - +
79A GLY* 1.3 78.9 - - - +
81A GLU* 1.3 69.6 + - - +
122B ARG* 3.1 34.5 + - - +
125B GLN* 4.4 3.9 + - - +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 3.7 29.7 - - - +
34A GLU 3.2 9.2 - - - +
35A LYS* 5.3 2.0 - - + -
36A ALA* 4.6 2.5 - - - +
74A GLY* 5.9 0.7 - - - -
79A GLY 5.4 1.8 - - - +
80A GLN* 1.3 85.1 - - - +
82A ARG* 1.3 67.1 + - - +
83A SER* 3.4 3.8 + - - -
206A CMP 4.2 2.9 + - - -
125B GLN* 5.9 0.7 + - - -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.4 34.9 - - + +
31A HIS 3.7 6.5 - - - +
32A GLN* 3.0 6.8 - - - +
33A GLY* 2.9 22.6 + - - +
34A GLU* 2.8 46.4 + - + +
35A LYS 4.4 1.0 + - - -
36A ALA* 3.7 12.8 - - - +
37A GLU 3.9 4.9 - - - +
38A THR* 3.0 35.7 + - - +
40A TYR* 3.8 17.1 + - - -
71A GLY* 3.1 12.6 + - - -
81A GLU* 1.3 72.9 - - - +
83A SER* 1.3 59.2 + - - +
84A ALA 3.5 0.9 - - - -
99A TYR* 2.9 22.4 + - - -
206A CMP 2.8 37.0 + - - +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.4 15.0 + - - +
51A ILE* 4.1 6.9 - - - +
73A LEU* 4.0 2.4 - - - +
81A GLU 3.4 3.2 + - - -
82A ARG* 1.3 71.9 - - - +
84A ALA* 1.3 59.1 + - - +
206A CMP 2.5 53.2 + - - -
125B GLN* 4.4 27.6 - - - -
128B SER* 5.9 5.4 - - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.4 22.0 - - - +
32A GLN* 3.5 17.3 - - - +
49A VAL* 3.9 25.1 - - + -
50A LEU 3.6 11.7 - - - +
51A ILE* 3.8 13.2 - - + -
61A LEU* 4.4 1.3 - - + -
82A ARG* 3.5 0.6 - - - +
83A SER* 1.3 81.5 + - - +
85A TRP* 1.3 59.3 + - - +
206A CMP 3.4 18.6 - - + +
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Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 4.2 13.0 - - + -
30A ILE 3.7 7.0 - - - -
31A HIS* 3.6 27.1 - - + +
32A GLN* 3.2 55.2 - - + +
48A ALA 3.6 0.3 - - - +
49A VAL* 3.3 3.8 - - - -
50A LEU* 2.8 61.9 + - + -
51A ILE* 4.3 2.2 - - - -
52A LYS* 3.9 53.4 - - + +
84A ALA* 1.3 73.8 - - - +
86A VAL* 1.3 61.5 + - - +
87A ARG* 4.0 10.5 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 4.1 1.0 - - - +
29A LEU* 3.3 28.4 + - + +
30A ILE* 3.4 38.9 + - + +
47A VAL* 3.6 31.0 - - + -
48A ALA 3.4 4.5 - - - +
49A VAL* 4.3 7.2 - - + -
70A ILE* 3.6 27.4 - - + -
85A TRP* 1.3 79.6 - - - +
87A ARG* 1.3 58.0 + - - +
206A CMP 3.6 23.6 - - - +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 4.4 22.2 - - - +
27A SER 3.5 9.2 - - - +
28A THR* 3.4 24.3 + - - +
47A VAL* 3.5 3.4 - - - -
48A ALA* 3.0 39.5 + - + +
50A LEU* 3.6 28.6 - - + +
52A LYS* 5.3 4.2 - - - +
58A GLU* 3.3 28.3 + - - -
85A TRP* 4.0 8.7 - - - +
86A VAL* 1.3 75.1 - - - +
88A ALA* 1.3 68.1 + - - +
89A LYS* 3.3 2.6 + - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.4 3.1 - - + -
24A PRO 3.6 13.9 - - - +
26A LYS* 2.8 30.8 + - - +
27A SER* 2.8 23.3 + - - +
29A LEU* 4.0 11.0 - - + +
46A SER 4.0 0.4 - - - -
47A VAL* 3.6 11.3 - - - +
87A ARG* 1.3 70.9 - - - +
89A LYS* 1.3 60.8 + - - +
90A THR 3.3 16.6 - - - +
92A CYS* 4.1 9.4 - - - -
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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