Contacts of the strand formed by residues 160 - 170 (chain A) in PDB entry 1VGU
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PRO* 4.1 2.3 - - - +
137A VAL* 3.4 31.3 + - + -
141A MET* 3.8 28.9 - - + -
155A VAL* 4.0 12.1 - - + -
156A ASP 3.6 18.6 - - - +
157A ARG* 3.1 21.0 + - - +
158A ASN 3.1 0.6 - - - -
159A GLY* 1.3 80.3 + - - +
161A TRP* 1.3 65.3 + - - +
141B MET* 4.1 17.0 - - + -
142B LYS 3.6 8.3 - - - +
143B ARG* 3.6 12.1 - - - +
155B VAL* 3.8 33.4 - - + -
160B LEU* 5.5 0.2 - - + -
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Residues in contact with TRP 161 (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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134A ALA* 3.8 22.2 - - + -
135A ALA 3.7 6.5 - - - -
136A PRO* 3.3 44.4 - - + -
137A VAL* 4.0 7.4 - - - -
159A GLY* 3.2 28.3 + - - -
160A LEU* 1.3 80.5 - - - +
162A HIS* 1.3 65.1 + - - +
204A LEU* 3.5 49.1 - - + +
206A GLU* 4.2 20.4 - - + -
141B MET* 3.0 26.3 - - - +
142B LYS* 2.8 23.5 + - + +
144B ALA* 4.0 6.1 - - - +
149B ASN* 3.9 22.7 - - - -
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 3.0 23.6 - - - +
135A ALA* 2.8 38.7 + - + +
136A PRO 3.6 13.2 + - - -
137A VAL* 3.9 16.7 - - + +
138A ARG 5.3 0.6 + - - -
139A ASP* 5.5 0.4 + - - -
161A TRP* 1.3 73.1 - - - +
163A ALA* 1.3 62.3 + - - +
164A LEU* 4.2 5.3 - - + +
209A ALA* 6.5 0.2 - - + -
139B ASP* 2.7 32.1 + - - +
140B THR 4.2 2.7 - - - -
141B MET* 3.6 16.9 - - - -
162B HIS* 3.9 28.3 - + - -
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Residues in contact with ALA 163 (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 ARG* 3.9 8.8 + - - -
132A ILE* 3.8 20.4 - - + -
133A LEU 4.3 0.2 - - - -
134A ALA* 4.4 0.2 - - - -
161A TRP 3.9 1.8 + - - -
162A HIS* 1.3 75.0 - - - +
164A LEU* 1.3 66.7 + - - +
167A GLN* 4.6 0.7 - - - +
190A ASP* 3.8 22.0 - - - +
139B ASP* 4.5 8.5 - - - +
140B THR* 3.0 31.6 + - + +
142B LYS* 4.0 10.0 - - + +
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Residues in contact with LEU 164 (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 ARG* 3.6 15.0 - - - +
133A LEU* 3.2 23.3 + - + +
134A ALA* 3.6 32.5 - - - +
135A ALA* 3.7 10.8 - - + +
162A HIS* 4.2 7.0 - - + +
163A ALA* 1.3 80.9 - - - +
165A THR* 1.3 72.5 - - - +
166A PRO 3.8 0.2 - - - +
167A GLN* 3.1 23.6 + - - +
207A GLY* 4.5 4.9 - - - +
208A ARG 4.0 18.8 - - - +
209A ALA 5.1 2.7 - - - +
211A ASN* 3.2 35.7 - - - +
139B ASP* 5.8 1.3 - - - +
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Residues in contact with THR 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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85A ARG* 5.4 7.4 - - - +
104A VAL 3.8 4.9 - - - +
105A HIS* 2.6 26.8 + - - -
106A ASP* 3.0 39.3 + - - +
109A ARG* 3.1 18.0 - - - +
133A LEU* 4.4 1.8 - - - -
164A LEU* 1.3 78.2 - - - +
166A PRO* 1.3 77.4 - - - +
167A GLN* 4.2 11.9 - - + +
190A ASP* 5.9 2.0 - - + -
211A ASN* 3.0 22.2 + - - -
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Residues in contact with PRO 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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45A LEU* 4.0 7.2 - - + -
103A LEU* 3.4 24.5 - - + -
104A VAL 3.2 10.3 - - - +
105A HIS* 3.2 17.4 - - + +
112A LEU* 3.2 35.7 - - + -
117A LEU* 4.1 7.2 - - + -
120A LEU* 3.6 7.5 - - + +
133A LEU* 3.4 38.9 + - + -
165A THR* 1.3 91.6 - - - +
167A GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 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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102A VAL 3.5 1.7 - - - +
103A LEU* 3.5 2.8 - - - -
104A VAL* 2.6 49.6 + - + +
131A GLY 3.8 5.2 - - - -
132A ILE* 3.3 25.3 - - + +
163A ALA* 4.6 1.8 - - - +
164A LEU 3.1 21.5 + - - +
165A THR* 4.0 10.4 - - + +
166A PRO* 1.3 79.7 - - - +
168A PHE* 1.3 60.5 + - - +
169A PHE* 3.5 14.3 - - + -
190A ASP* 3.3 29.1 + - - +
191A GLU* 3.6 8.9 + - - +
192A ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 168 (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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8A VAL* 3.7 28.7 - - + -
50A ARG* 4.2 2.2 - - - -
101A TRP* 3.3 52.5 - + + -
102A VAL 3.2 16.6 - - - -
103A LEU* 4.0 12.1 - - + -
120A LEU* 3.7 33.8 - - + +
121A LEU* 3.7 26.5 - - + -
123A LEU* 4.6 2.2 - - + -
124A SER* 3.5 20.4 - - - -
130A GLY* 3.2 2.8 - - - -
131A GLY 2.9 42.6 + - - +
167A GLN* 1.3 71.4 - - - +
169A PHE* 1.3 66.1 + - - +
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Residues in contact with PHE 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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101A TRP* 3.2 10.7 - - - -
102A VAL* 2.9 31.6 + - - +
104A VAL* 4.6 2.5 - - + -
129A THR 3.5 15.3 - - - -
131A GLY 4.6 0.9 - - - -
132A ILE* 4.2 3.8 - - + -
167A GLN* 3.5 33.9 - - + -
168A PHE* 1.3 80.0 - - - +
170A PRO* 1.3 79.3 - - + +
174A LEU* 4.1 30.1 - - + +
191A GLU* 3.6 19.7 - - + -
192A ALA* 3.4 36.1 - - + -
195A LEU* 3.9 19.3 - - + -
202A PRO* 4.1 14.4 - - + -
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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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100A GLN* 3.5 11.9 - - + +
101A TRP* 3.6 32.3 - - + +
128A ARG* 3.4 30.3 - - - +
129A THR 4.0 9.4 - - - +
169A PHE* 1.3 89.5 - - + +
171A ARG* 1.3 65.8 + - - +
172A GLU* 3.6 1.3 - - + +
173A LEU* 3.5 20.5 + - + +
174A LEU* 3.3 18.4 + - - +
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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