Contacts of the strand formed by residues 57 - 65 (chain D) in PDB entry 1GQT
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 ASN 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ALA* 2.5 42.1 + - - +
5D GLY 4.1 5.9 + - - +
6D SER* 3.3 11.5 - - - -
7D LEU 2.6 32.7 + - - -
55D GLY 4.7 3.8 + - - +
56D ALA* 1.3 74.5 - - - +
58D ILE* 1.3 51.7 + - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 3.0 22.7 - - + +
9D VAL* 3.7 17.7 - - + -
48D ALA* 3.6 32.3 - - + +
51D ALA* 4.5 2.0 - - + -
52D GLY* 3.7 32.8 - - - +
56D ALA* 3.6 10.5 + - + +
57D ASN* 1.3 74.6 - - - +
59D ALA* 1.3 80.3 + - - +
81D ASN 3.7 12.5 + - - +
82D ILE* 3.9 10.7 - - + -
83D ASP* 3.2 24.8 + - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU 2.7 9.2 + - - +
8D VAL* 3.3 7.7 - - + -
9D VAL 2.8 25.1 + - - +
58D ILE* 1.3 79.2 - - - +
60D PHE* 1.3 60.8 + - - +
83D ASP* 3.5 20.4 - - + +
86D PRO* 4.4 2.2 - - + -
131D ARG* 3.9 35.4 - - - +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.3 23.1 - - + -
11D GLY 3.7 28.3 - - - -
13D ILE* 3.6 27.4 - - + -
44D GLY 3.6 10.8 - - - -
45D ALA* 3.4 32.5 - - + -
48D ALA* 4.1 11.7 - - + -
59D ALA* 1.3 75.3 - - - +
61D ILE* 1.3 62.9 + - - +
62D ALA* 3.6 12.8 - - + -
77D LEU* 3.9 17.3 - - + -
82D ILE* 3.9 19.7 - - + -
83D ASP 3.3 6.7 + - - +
86D PRO* 3.2 23.8 - - - +
87D VAL* 3.6 18.1 - - + +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.7 27.1 - - + -
9D VAL 2.7 11.6 + - - +
10D LEU* 3.2 24.7 - - + +
11D GLY 3.1 26.3 + - - -
60D PHE* 1.3 73.8 - - - +
62D ALA* 1.3 63.0 + - - +
86D PRO* 3.7 25.1 - - + +
120D LEU* 3.7 11.1 - - + +
124D LEU* 5.3 7.2 - - + +
125D VAL* 5.6 2.2 - - - -
128D GLN* 3.7 36.8 - - + +
131D ARG* 4.6 3.6 - - - -
132D ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY 3.1 24.9 - - - +
12D SER* 5.1 0.2 - - - -
13D ILE* 3.8 17.5 - - + -
60D PHE* 3.6 22.9 + - + -
61D ILE* 1.3 75.2 - - - +
63D CYS* 1.3 61.0 + - - +
86D PRO 3.6 4.6 + - - +
87D VAL* 3.3 5.6 - - + +
88D SER* 2.7 33.1 + - - -
120D LEU* 3.9 7.4 - - - -
124D LEU* 5.7 0.2 - - - +
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Residues in contact with CYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY 4.8 0.4 + - - -
13D ILE* 4.4 9.2 - - - +
62D ALA* 1.3 80.3 - - - +
64D THR* 1.3 60.6 + - - +
88D SER* 3.2 7.6 - - - -
90D ILE* 3.9 19.5 - - + -
95D THR* 5.5 0.7 - - - +
96D GLY 5.7 0.2 + - - -
116D ALA* 3.3 24.5 - - - +
117D ASN* 3.7 20.0 + - - +
119D ALA 4.1 2.2 - - - -
120D LEU* 3.8 28.3 - - - +
124D LEU* 3.7 29.8 - - - -
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.9 22.2 - - + -
63D CYS* 1.3 73.2 - - - +
65D GLY* 1.3 69.2 + - - +
70D GLY* 4.0 4.2 + - - +
73D VAL* 3.9 14.4 - - + -
74D ARG* 3.6 38.1 + - + -
87D VAL* 4.1 3.6 - - + +
88D SER 3.0 9.4 + - - +
89D VAL* 3.9 2.9 - - - +
90D ILE* 2.9 24.3 + - - +
95D THR* 3.4 15.3 - - - -
116D ALA* 3.3 13.7 - - - +
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Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D THR* 1.3 88.7 + - - +
66D ASP* 1.3 58.3 + - - -
67D ASP* 3.1 13.0 + - - +
70D GLY* 4.1 5.4 - - - -
74D ARG* 5.2 0.9 + - - -
89D VAL* 3.8 5.5 - - - +
90D ILE 3.8 5.6 - - - -
93D GLU 3.0 17.9 - - - -
94D SER 3.8 8.5 - - - -
95D THR* 2.8 15.0 + - - +
116D ALA* 3.5 6.5 - - - +
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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