Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 1GQR
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 TYR 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY* 3.3 23.1 - - - -
33A ILE 3.2 6.1 - - - +
34A PRO* 3.4 31.1 - - + +
35A PHE* 3.5 7.8 - - - -
38A PRO* 4.7 4.0 - - + +
51A LYS* 5.8 1.4 + - - -
58A TRP* 4.0 19.1 - + - -
64A PRO* 3.7 36.4 - - + +
65A ASN* 5.4 1.8 - - + -
93A ASP* 2.6 50.6 + - - -
94A CYS* 3.0 17.3 + - - +
95A LEU* 1.3 80.6 - - - +
97A LEU* 1.3 61.1 + - - +
125A SER* 5.0 2.1 + - - -
146A LEU 4.0 0.7 - - - -
147A SER* 2.8 23.8 + - - -
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Residues in contact with LEU 97 (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 GLY 3.3 2.9 + - - -
33A ILE* 2.8 52.2 + - + +
35A PHE* 3.9 25.8 - - + -
96A TYR* 1.3 76.2 - - - +
98A ASN* 1.3 64.9 + - - +
99A ILE* 3.7 33.2 - - + -
144A VAL* 4.5 6.5 - - + -
145A SER 3.4 13.5 - - - +
146A LEU* 4.2 6.1 - - - -
176A ALA* 4.2 17.5 - - + +
179A TRP* 3.9 25.4 - - + -
180A VAL* 4.5 7.9 - - + -
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Residues in contact with ASN 98 (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 PHE 3.3 4.3 - - - -
31A LEU* 3.6 10.5 - - + -
32A GLY 3.0 25.3 + - - -
63A TYR* 3.6 20.1 - - - -
64A PRO* 3.3 15.7 - - - +
96A TYR 5.3 0.2 + - - -
97A LEU* 1.3 74.4 - - - +
99A ILE* 1.3 66.3 + - - +
100A TRP* 3.8 15.6 - - + -
125A SER* 3.1 24.4 + - - -
143A LEU 3.8 0.3 - - - +
144A VAL* 3.2 5.9 - - - +
145A SER* 2.9 52.7 + - - +
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Residues in contact with ILE 99 (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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29A ALA* 3.4 4.2 - - - +
30A PHE* 2.8 47.0 + - + +
31A LEU* 4.7 0.2 - - - +
33A ILE* 3.7 23.6 - - + -
97A LEU* 3.7 18.6 - - + -
98A ASN* 1.3 81.2 - - - +
100A TRP* 1.3 65.6 + - - +
101A VAL* 3.7 13.2 - - + -
142A VAL* 3.5 30.5 - - + -
143A LEU 3.4 4.9 - - - +
144A VAL* 4.0 9.6 - - + -
179A TRP* 4.0 9.4 - - + -
180A VAL* 6.1 0.2 - - + -
184A ILE* 4.1 9.4 - - + -
187A PHE* 3.9 22.0 - - + -
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Residues in contact with TRP 100 (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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20A VAL* 5.4 3.0 - - + +
27A ILE* 3.8 12.3 - - + -
28A SER 3.5 1.8 - - - -
29A ALA* 4.1 19.2 - - + +
31A LEU* 3.9 15.1 - - + +
63A TYR* 3.2 28.9 - + - -
98A ASN* 3.8 21.3 - - + -
99A ILE* 1.3 74.8 - - - +
101A VAL* 1.3 61.0 + - - +
125A SER 5.0 1.6 - - - -
130A TYR 4.2 5.6 - - - -
131A ASN* 3.5 16.9 + - - -
132A GLY* 3.7 30.3 - - - +
133A LYS* 3.6 20.2 - - + +
136A ALA* 3.7 20.6 - - + -
141A VAL 3.8 3.6 - - - +
142A VAL* 3.5 6.4 - - - +
143A LEU* 2.8 49.4 + - + +
144A VAL 5.1 0.2 - - - -
145A SER* 3.6 26.0 - - - -
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Residues in contact with VAL 101 (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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27A ILE* 3.6 4.1 - - - +
28A SER* 2.9 40.3 + - - +
30A PHE* 3.8 24.0 - - + -
99A ILE* 3.7 22.2 - - + -
100A TRP* 1.3 76.2 - - - +
102A PRO* 1.3 79.8 - - + +
105A ARG* 4.0 10.5 - - + +
106A PRO* 3.6 9.9 - - + -
136A ALA* 5.4 0.4 - - - -
142A VAL* 4.1 3.8 - - + -
187A PHE* 3.2 39.7 - - + +
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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