Contacts of the strand formed by residues 164 - 174 (chain A) in PDB entry 2VSH
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 LEU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU* 4.2 2.6 - - - +
142A ALA* 3.3 27.1 + - + +
146A ILE* 3.9 30.5 - - + +
159A PRO* 3.7 33.9 - - + +
160A ASN 3.5 10.8 - - - +
161A ARG* 3.3 28.3 + - + +
162A ALA 3.6 0.9 - - - -
163A HIS* 1.3 86.0 - - - +
165A TYR* 1.3 68.1 + - - +
146B ILE* 3.9 20.0 - - + -
147B VAL 3.5 0.7 - - - -
148B GLU* 4.3 17.9 - - + +
159B PRO* 5.6 3.8 - - + -
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Residues in contact with TYR 165 (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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139A VAL* 3.7 30.5 - - + -
140A VAL 3.1 22.2 - - - +
141A GLU* 4.0 18.2 - - + -
142A ALA* 3.7 5.6 - - - +
162A ALA 4.9 6.3 + - - -
163A HIS* 3.7 17.7 - - - -
164A LEU* 1.3 77.2 - - - +
166A GLN* 1.3 59.2 + - - +
209A LEU* 4.0 14.1 - - + -
146B ILE* 3.5 8.7 - - - +
147B VAL* 2.8 45.7 + - + +
149B SER* 3.9 26.3 + - - -
152B GLY* 3.7 19.4 + - - -
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Residues in contact with GLN 166 (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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115A ARG* 4.9 4.0 + - - -
139A VAL* 3.3 4.6 - - - -
140A VAL* 2.7 46.8 + - + +
141A GLU 4.8 0.4 + - - +
142A ALA* 3.8 12.8 - - + +
143A VAL 6.0 1.4 - - - +
144A ASP* 5.7 2.0 + - - -
165A TYR* 1.3 71.2 - - - +
167A GLY* 1.3 67.8 + - - +
168A GLN* 3.3 29.1 + - - +
214A TYR* 5.4 7.3 - - - -
144B ASP* 3.4 38.2 + - + +
145B THR 4.0 2.7 - - - -
146B ILE* 4.5 6.1 - - + -
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Residues in contact with GLY 167 (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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115A ARG* 3.8 8.8 + - - -
137A ASP* 5.0 1.8 - - - -
138A THR 4.1 3.1 - - - -
139A VAL* 4.1 9.2 - - - -
165A TYR 3.7 1.8 + - - -
166A GLN* 1.3 78.5 - - - +
168A GLN* 1.3 64.9 + - - +
144B ASP* 4.6 5.7 - - - +
145B THR* 2.8 31.9 + - - +
147B VAL* 4.2 10.7 - - - +
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.7 18.2 - - - +
137A ASP* 3.6 12.8 - - - +
138A THR 2.7 22.9 + - - +
139A VAL* 4.6 0.4 - - - -
140A VAL* 3.7 15.6 - - - +
166A GLN* 3.3 31.1 + - - +
167A GLY* 1.3 79.7 - - - +
169A THR* 1.3 72.1 + - - +
171A GLN* 4.1 3.6 - - - +
212A GLY* 3.2 9.4 - - - -
213A GLU 2.8 42.8 + - - -
214A TYR* 4.6 3.0 + - - +
216A ASN* 3.2 27.9 + - - +
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Residues in contact with THR 169 (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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85A ARG* 3.9 21.1 - - - +
110A THR* 4.0 1.1 - - - +
111A HIS* 2.7 34.3 + - - +
112A ASP* 3.0 29.3 + - - +
115A ARG* 3.5 10.0 - - - +
138A THR* 3.8 4.5 - - - -
168A GLN* 1.3 82.8 - - - +
170A PRO* 1.4 75.6 - - - +
171A GLN* 4.2 12.6 - - + -
216A ASN* 2.8 24.1 + - - -
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Residues in contact with PRO 170 (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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109A VAL* 3.6 24.0 - - + -
110A THR 3.0 15.7 - - - +
111A HIS* 3.5 9.0 - - + +
118A ILE* 3.4 31.6 - - + -
122A MET* 4.8 4.3 - - + -
123A ILE* 5.0 3.6 - - - -
126A ASN* 3.4 24.6 - - + +
138A THR* 2.7 45.5 + - + +
169A THR* 1.4 81.8 - - - +
171A GLN* 1.3 60.6 + - - +
172A THR* 3.9 0.2 - - - +
216A ASN* 4.9 0.4 - - - +
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Residues in contact with GLN 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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85A ARG* 4.4 17.6 - - - +
89A ILE* 5.3 1.0 - - - +
110A THR* 2.6 48.4 + - - +
136A VAL 3.2 5.4 - - - -
137A ASP* 3.2 23.5 - - - +
168A GLN 4.1 10.2 - - - +
169A THR* 4.2 9.2 - - + -
170A PRO* 1.3 77.7 - - - +
172A THR* 1.3 61.4 + - - +
173A PHE* 3.8 8.1 - - + -
195A ASP* 3.0 25.9 + - - +
196A ALA* 3.6 28.3 - - - +
197A CYS* 3.7 17.7 - - - -
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Residues in contact with THR 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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107A ILE* 3.6 25.8 - - + -
108A VAL 3.4 6.5 - - - +
109A VAL* 3.6 21.9 - - + +
126A ASN* 2.7 38.3 + - - +
127A ILE 4.8 0.4 - - - +
130A ALA* 3.7 17.4 - - + +
135A ALA* 3.1 3.6 - - - +
136A VAL* 2.8 41.6 + - - +
171A GLN* 1.3 73.4 - - - +
173A PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 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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89A ILE* 4.0 8.3 - - + -
107A ILE* 4.3 6.7 - - - -
108A VAL* 2.9 48.8 + - + -
110A THR* 3.7 20.0 - - + -
130A ALA* 5.3 3.6 - - - -
134A ASP 3.8 12.3 - - - +
135A ALA* 3.9 6.5 - - + -
171A GLN* 3.8 16.8 - - + -
172A THR* 1.3 84.3 - - - +
174A ARG* 1.3 66.4 + - - +
178A PHE* 3.6 42.2 - + + -
196A ALA* 3.7 24.7 - - + -
197A CYS* 5.3 2.2 - - - -
200A PHE* 3.6 28.9 - + + -
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Residues in contact with ARG 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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104A PRO 3.5 27.4 - - - +
105A GLU* 3.1 29.1 + - - +
106A ASP 3.3 11.0 - - - +
107A ILE* 4.0 15.3 - - + +
130A ALA* 2.6 26.6 + - - +
131A GLN* 3.5 17.2 + - - +
132A ASN 5.5 0.2 - - - -
133A HIS 2.8 24.5 + - - +
134A ASP* 3.7 20.4 + - - +
173A PHE* 1.3 77.4 - - - +
175A CYS* 1.3 64.9 + - - +
176A LYS 4.5 0.2 - - - +
177A ASP* 3.2 30.5 + - + +
178A PHE 3.1 18.2 + - - -
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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
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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