Contacts of the strand formed by residues 108 - 113 (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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLY* 2.8 33.8 + - - +
29A GLU 4.9 1.2 + - - -
24B PHE* 3.9 0.2 - - - -
100B ILE* 4.3 2.0 - - + -
101B PHE 3.1 11.2 - - - +
102B VAL* 4.2 7.0 - - + -
106B GLY 4.8 2.8 - - - +
107B GLU* 1.3 79.2 - - - +
109B VAL* 1.3 67.3 + - - +
110B ILE* 3.5 27.7 - - - +
250B THR* 4.7 9.7 + - - +
251B ILE* 3.5 33.4 - - + +
1310B ACP 5.5 3.1 + - - -
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Residues in contact with VAL 109 (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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25A PRO* 3.0 43.3 - - + +
26A THR 3.8 7.6 - - - +
27A PRO* 3.6 24.7 - - + -
29A GLU 3.9 3.6 - - - -
101A PHE* 4.4 10.4 - - + -
24B PHE* 3.8 23.3 - - + -
99B LEU 3.8 0.3 - - - +
100B ILE* 3.3 6.2 - - - +
101B PHE* 2.8 38.2 + - + +
108B ASN* 1.3 81.2 - - - +
110B ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 110 (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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25A PRO* 4.0 5.1 - - - +
29A GLU 3.2 4.9 + - - +
30A THR* 3.3 26.6 - - + +
31A VAL* 3.1 26.7 + - - +
43B LYS* 5.3 1.3 - - - +
98B ALA* 4.1 10.5 - - + -
99B LEU 3.4 6.3 - - - +
100B ILE* 4.0 15.7 - - + -
108B ASN* 3.5 22.4 - - - +
109B VAL* 1.3 82.5 - - - +
111B GLY* 1.3 64.6 + - - +
112B ILE* 3.8 25.8 - - + -
251B ILE* 5.5 1.8 - - + -
1311B RIB 4.1 30.7 - - + +
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Residues in contact with GLY 111 (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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19A LEU* 3.4 19.9 - - - +
21A LEU* 4.5 0.2 - - - -
31A VAL* 3.4 13.5 - - - -
101A PHE* 3.7 14.3 - - - -
98B ALA* 3.3 2.4 - - - +
99B LEU* 2.7 38.4 + - - +
110B ILE* 1.3 73.6 - - - +
112B ILE* 1.3 61.7 + - - -
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Residues in contact with ILE 112 (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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19A LEU* 3.5 7.0 - - - +
30A THR* 4.0 14.4 - - + -
31A VAL 2.9 12.0 + - - +
32A THR* 3.4 15.4 - - + +
33A GLY 2.8 26.5 + - - -
14B ASN* 3.7 13.0 - - - +
97B VAL 3.5 3.8 - - - +
98B ALA* 3.9 9.6 - - + -
110B ILE* 3.8 13.0 - - + -
111B GLY* 1.3 79.1 - - - +
113B HIS* 1.3 75.0 + - - +
114B ALA* 3.8 8.3 - - + +
117B ASN* 5.9 0.7 - - - +
143B GLU* 3.4 34.8 - - + +
1311B RIB 3.5 12.8 - - - +
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Residues in contact with HIS 113 (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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19A LEU* 3.8 18.7 - - + +
33A GLY 5.0 4.5 + - - +
34A ASN 5.9 0.8 - - - -
35A HIS* 5.1 3.2 + - - -
36A TYR* 3.5 44.6 + + + +
94B SER* 3.6 20.5 + - - -
95B THR 4.4 7.0 - - - -
96B GLY* 3.4 0.9 - - - -
97B VAL* 2.8 43.7 + - + +
112B ILE* 1.3 75.4 - - - +
114B ALA* 1.3 64.9 + - - +
115B GLY* 3.9 19.6 + - - -
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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