Contacts of the strand formed by residues 14 - 20 (chain B) 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 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 4.8 0.6 + - - -
13B ILE* 1.3 87.3 - - - +
15B ALA* 1.3 60.8 + - - +
16B ASP* 3.9 6.1 - - - +
40B PHE* 3.8 7.2 - - - -
41B GLY 2.8 32.7 + - - +
42B GLY* 3.7 13.7 - - - +
69B ILE* 5.8 0.9 - - - -
95B THR* 4.8 2.2 - - - -
96B GLY* 3.2 18.2 - - - +
97B VAL 3.7 6.2 + - - +
98B ALA* 4.0 3.5 - - - +
112B ILE* 3.7 19.5 - - - +
113B HIS 4.6 1.6 - - - +
117B ASN* 3.1 16.0 + - - -
143B GLU* 4.1 4.2 + - - +
1311B RIB 3.2 32.2 + - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 1.3 73.3 - - - +
16B ASP* 1.3 62.7 + - - +
17B HIS* 3.8 15.4 - - - +
38B VAL* 4.9 9.4 - - + -
39B ALA 3.6 5.8 - - - +
40B PHE* 4.9 2.9 - - + +
69B ILE* 4.2 24.7 - - + -
95B THR* 4.8 1.2 - - - +
96B GLY 2.9 11.9 + - - +
97B VAL* 3.4 8.2 - - + -
98B ALA 2.9 23.4 + - - +
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 3.9 0.9 - - - +
15B ALA* 1.3 72.7 - - - +
17B HIS* 1.3 61.5 + - - +
18B ILE* 3.8 21.2 - - + +
37B GLN 3.5 1.0 - - - +
38B VAL* 3.2 10.7 - - - +
39B ALA* 2.7 36.8 + - + +
40B PHE 4.1 0.2 - - - +
41B GLY* 3.5 14.9 - - - -
98B ALA* 3.5 11.2 - - - +
100B ILE* 3.8 11.2 - - + +
251B ILE* 4.8 0.5 - - - +
291B ALA* 4.0 9.2 - - - +
1311B RIB 2.5 47.8 + - - -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 3.8 25.0 + + - -
36A TYR* 4.4 3.8 + - - -
99A LEU* 3.7 12.7 - - + +
15B ALA* 3.8 11.2 + - - +
16B ASP* 1.3 78.3 - - - +
18B ILE* 1.3 56.7 + - - +
36B TYR* 2.7 27.2 + - + +
37B GLN 3.7 3.1 - - - -
38B VAL* 3.9 20.3 - - + +
97B VAL* 3.7 31.2 - - + +
98B ALA 2.8 12.6 + - - +
99B LEU* 3.7 16.1 - - + -
100B ILE* 2.7 33.1 + - - +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.8 23.1 - - + +
17B HIS* 1.3 76.0 - - - +
19B LEU* 1.3 65.0 + - - +
20B ASN* 4.2 8.6 + - - +
35B HIS 3.6 0.9 - - - +
36B TYR* 3.2 9.3 - - - -
37B GLN* 2.9 54.1 + - + +
39B ALA* 4.9 4.3 - - + -
100B ILE* 3.4 27.4 - - + +
102B VAL* 4.0 25.4 - - + -
249B ASP* 5.3 6.3 - - - +
251B ILE* 5.1 8.1 - - + -
289B LYS* 5.7 2.7 - - - +
290B GLY* 4.3 25.1 - - - +
291B ALA 5.0 1.3 - - - +
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Residues in contact with LEU 19 (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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99A LEU* 4.1 14.8 - - + -
111A GLY* 3.4 39.9 - - - +
112A ILE 3.4 15.3 - - - +
113A HIS* 4.1 15.9 - - + -
17B HIS 4.2 0.2 + - - -
18B ILE* 1.3 75.3 - - - +
20B ASN* 1.3 64.2 + - - +
21B LEU* 3.7 13.7 + - + +
33B GLY* 3.9 19.7 - - - +
35B HIS 3.2 19.3 - - - +
36B TYR* 4.3 4.7 - - + -
100B ILE 2.9 13.3 + - - +
101B PHE* 3.6 10.8 - - + -
102B VAL 3.2 20.0 + - - -
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.1 6.4 - - - +
19B LEU* 1.3 71.8 - - - +
21B LEU* 1.3 56.4 + - - +
33B GLY* 3.0 6.4 - - - -
34B ASN* 2.7 50.9 + - - +
35B HIS* 2.7 28.3 + - - +
102B VAL* 3.5 34.5 + - - +
103B ASN 5.2 0.8 + - - -
248B VAL 5.6 2.8 + - - -
249B ASP* 5.7 2.4 + - - +
289B LYS* 3.1 30.2 + - - +
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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
------------------------------------------------------------
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