Contacts of the strand formed by residues 79 - 86 (chain A) in PDB entry 1GCF
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 VAL 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLN* 2.8 67.9 + - + +
77A ALA* 3.6 2.8 - - - +
78A PRO* 1.3 89.6 - - + +
80A TYR* 1.3 71.4 + - - +
103A GLN* 4.4 2.0 - - + -
104A LEU* 3.2 25.4 - - - +
105A ARG* 4.0 15.9 - - + +
106A PRO* 4.5 1.6 - - - -
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Residues in contact with TYR 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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26A LEU* 5.1 3.6 - - + -
47A TYR* 4.0 27.4 - + + -
48A GLN 3.3 16.2 - - - -
49A PRO* 3.4 30.8 - - + +
73A GLY 4.9 0.3 + - - -
74A LEU* 3.5 30.5 - - + -
75A HIS* 3.2 20.4 + - - -
76A GLN* 4.0 8.2 + - - +
77A ALA 4.3 18.4 - - - -
79A VAL* 1.3 81.7 - - - +
81A THR* 1.3 62.2 + - - +
82A LEU* 4.0 12.7 - - + +
103A GLN* 3.4 2.8 - - - -
104A LEU 3.0 31.1 + - - +
106A PRO* 3.3 33.1 - - + +
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Residues in contact with THR 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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47A TYR* 3.2 0.9 - - - +
48A GLN* 3.0 41.6 + - - +
50A GLN* 3.1 31.6 + - - +
56A TRP* 3.6 28.0 - - + -
80A TYR* 1.3 72.1 + - - +
82A LEU* 1.3 77.7 + - - +
83A GLN* 3.6 13.7 - - - +
102A LEU 3.8 7.2 - - - +
103A GLN* 3.8 10.0 - - + +
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Residues in contact with LEU 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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9A LEU* 4.4 3.5 - - + +
26A LEU* 5.1 11.9 - - + -
28A LEU* 3.7 39.3 - - + -
45A LEU* 4.6 4.5 - - + -
46A ARG 3.1 7.4 - - - +
47A TYR* 3.6 20.4 - - + +
56A TRP* 5.4 0.2 - - - -
71A LEU* 5.4 3.8 - - + -
80A TYR* 4.0 15.7 - - + +
81A THR* 1.3 109.3 - - - +
83A GLN* 1.3 73.8 + - - +
101A GLY* 3.1 3.1 - - - -
102A LEU* 3.0 43.3 + - + +
103A GLN* 5.4 0.4 - - - -
104A LEU 5.5 1.6 - - - +
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Residues in contact with GLN 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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9A LEU* 5.1 1.4 - - - +
45A LEU* 3.0 24.8 - - - +
46A ARG* 3.0 14.9 + - + +
56A TRP* 4.2 21.0 - - + -
81A THR* 3.6 15.9 - - - +
82A LEU* 1.3 97.3 - - - +
84A MET* 1.3 61.2 + - - +
98A TRP* 3.9 23.1 - - + +
99A SER 2.8 23.3 - - - +
100A PRO* 3.6 7.4 - - + +
101A GLY* 3.4 17.9 + - - +
102A LEU 4.1 2.4 + - - -
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Residues in contact with MET 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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9A LEU* 3.8 21.1 - - + -
30A TRP* 2.9 76.1 - - + +
43A CYS* 5.7 0.4 - - + -
44A GLU 3.5 7.9 - - - +
45A LEU* 3.2 32.1 - - + -
83A GLN* 1.3 77.0 - - - +
85A ARG* 1.3 65.0 + - - +
86A CYS* 5.1 7.9 - - - -
98A TRP* 3.1 9.1 - - - -
99A SER* 3.0 44.0 + - - +
101A GLY 4.9 0.2 - - - +
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Residues in contact with ARG 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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44A GLU* 3.2 30.4 + - + +
84A MET* 1.3 74.4 - - - +
86A CYS* 1.3 74.2 + - - +
94A PHE 5.1 1.2 + - - -
95A TRP* 3.3 42.1 - - + +
96A SER 3.4 20.8 + - - +
97A PRO* 4.3 7.0 - - - +
98A TRP* 2.7 73.0 - - + +
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Residues in contact with CYS 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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30A TRP* 6.0 1.6 - - - -
32A PRO* 5.6 7.4 - - - -
41A GLN* 5.0 4.7 - - - +
42A GLU 3.9 1.1 - - - -
43A CYS* 2.0 48.7 - - - +
64A SER 5.3 1.3 - - - -
84A MET* 5.1 8.1 - - - -
85A ARG* 1.3 83.1 - - - +
87A ILE* 1.3 68.3 + - - +
95A TRP* 3.1 28.2 + - - +
96A SER* 4.6 6.9 - - - -
97A PRO 5.5 0.4 + - - -
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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