Contacts of the strand formed by residues 170 - 178 (chain A) in PDB entry 3Q2T
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 GLU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A MET* 4.0 10.5 - - - +
76A MET* 3.9 4.5 - - - -
77A ARG* 3.5 34.8 + - + -
79A THR* 3.1 22.3 + - - +
148A TRP 4.1 0.3 - - - +
149A TRP* 3.6 4.0 - - - +
150A ARG* 2.6 79.0 + - + +
157A GLN* 4.5 4.7 - - - -
168A PRO* 3.4 2.6 - - - +
169A LYS* 1.3 83.5 - - - +
171A HIS* 1.3 65.5 - - - +
172A LYS* 4.3 13.9 + - - +
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Residues in contact with HIS 171 (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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76A MET* 3.5 22.4 - - - +
77A ARG 2.8 12.0 + - - +
78A ARG* 3.6 9.1 - - + +
79A THR* 2.8 27.7 + - - +
117A GLU* 4.9 6.3 + - - -
147A ASN* 2.9 32.6 + - - -
148A TRP 3.6 6.1 - - - -
149A TRP* 3.5 30.8 + + + -
170A GLU* 1.3 77.6 - - - +
172A LYS* 1.3 83.9 + - - +
173A LYS* 4.4 16.4 - - + -
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Residues in contact with LYS 172 (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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79A THR* 3.2 30.5 - - + +
81A GLU* 3.1 39.4 + - + +
146A GLY 3.9 0.3 - - - +
147A ASN* 3.3 6.4 - - - +
148A TRP* 2.8 49.2 + - + +
150A ARG* 5.0 3.2 - - - +
157A GLN* 3.8 25.7 + - - +
170A GLU* 4.3 10.7 + - + +
171A HIS* 1.3 75.4 - - - +
173A LYS* 1.3 60.9 + - - +
174A LEU* 4.2 4.4 + - + +
211A ILE* 4.0 17.5 - - + +
2E U 5.8 1.6 + - - -
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Residues in contact with LYS 173 (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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79A THR 2.8 10.4 + - - +
80A VAL* 3.3 8.6 - - + -
81A GLU 3.1 23.4 + - - +
117A GLU* 3.5 36.5 + - - +
144A CYS* 3.3 32.5 - - - -
147A ASN* 3.0 27.4 - - - +
171A HIS* 4.2 12.2 - - + +
172A LYS* 1.3 73.0 - - - +
174A LEU* 1.3 67.8 + - - +
175A PHE* 3.8 20.0 - - + -
33B LEU* 4.6 9.6 + - - +
34B GLU* 4.6 19.4 + - - +
221B ARG 5.5 1.3 + - - -
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Residues in contact with LEU 174 (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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81A GLU* 3.3 38.4 - - + +
83A VAL* 4.8 2.0 - - + -
106A LEU* 4.4 13.9 - - + -
144A CYS* 3.2 7.6 - - - -
145A ILE* 2.6 47.0 + - + -
146A GLY* 2.8 23.3 + - - +
148A TRP* 4.8 9.2 - - + +
172A LYS* 5.0 5.8 - - + +
173A LYS* 1.3 85.0 - - - +
175A PHE* 1.3 60.4 + - - +
211A ILE* 3.7 30.3 - - + -
215A LEU* 4.5 14.1 - - + -
218A LEU* 5.7 2.2 - - + -
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Residues in contact with PHE 175 (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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80A VAL* 3.7 26.9 - - + -
81A GLU 3.0 7.0 + - - -
82A GLY* 3.4 4.0 - - - -
83A VAL* 2.9 23.3 + - - +
117A GLU* 4.0 26.2 - - + -
118A VAL* 4.5 6.5 - - + -
121A LEU* 3.5 24.0 - - + -
141A ILE* 3.6 26.9 - - + -
143A ASP 3.1 18.2 - - - +
144A CYS* 3.8 14.4 - - + -
145A ILE* 4.5 2.5 - - - -
173A LYS* 3.8 27.6 - - + -
174A LEU* 1.3 74.2 - - - +
176A LEU* 1.3 65.1 + - - +
177A VAL* 3.3 0.9 + - + +
33B LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 176 (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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37A ILE* 3.9 33.2 - - + -
83A VAL* 3.3 21.5 - - + +
85A ILE* 3.8 20.0 - - + -
140A VAL 4.2 4.5 - - - +
141A ILE* 4.2 6.8 - - - -
142A ASP 4.6 0.3 + - - -
143A ASP* 3.0 24.8 + - + +
145A ILE* 3.4 24.9 - - + +
175A PHE* 1.3 75.7 - - - +
177A VAL* 1.3 78.8 + - - +
178A GLN* 4.1 7.1 + - + +
219A LEU* 5.0 4.3 - - + -
222A PHE* 3.6 33.0 - - + -
224A PHE* 5.1 2.2 - - + -
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Residues in contact with VAL 177 (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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82A GLY* 4.1 4.7 - - - -
83A VAL 3.2 11.3 + - - +
84A LEU* 3.7 38.8 - - + -
85A ILE 4.0 4.9 + - - -
121A LEU* 4.4 0.9 - - + -
125A MET* 3.7 26.5 - - + -
139A TRP* 4.4 15.3 - - + -
140A VAL 3.8 5.4 - - - +
141A ILE* 3.7 27.1 - - + -
175A PHE 3.3 9.4 + - - +
176A LEU* 1.3 81.3 - - - +
178A GLN* 1.3 72.7 + - - +
179A LEU* 3.7 3.8 + - + +
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Residues in contact with GLN 178 (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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35A ARG* 3.3 17.4 - - - +
37A ILE* 3.4 34.0 - - + +
38A ASN* 5.0 12.2 + - - +
139A TRP* 5.6 0.5 - - - -
140A VAL* 3.2 42.7 + - + +
142A ASP* 3.2 29.4 + - - +
143A ASP* 4.1 0.6 + - - +
176A LEU* 4.8 9.2 - - + +
177A VAL* 1.3 78.5 - - - +
179A LEU* 1.3 69.6 + - - +
180A GLN* 4.4 5.0 - - - +
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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