Contacts of the strand formed by residues 171 - 177 (chain B) in PDB entry 1VDG
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 TRP 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 3.3 9.9 - - - +
136B GLU* 2.9 46.0 + - + +
169B ARG* 3.5 57.3 + - + +
170B TRP* 1.3 82.2 - - - +
172B TYR* 1.3 65.4 + - - +
191B LEU* 3.4 34.3 - - + -
192B LEU 3.7 2.0 - - - -
193B GLU* 3.0 47.3 + - + +
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Residues in contact with TYR 172 (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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104B LEU* 3.5 12.8 - - + +
120B LEU* 3.8 15.0 - - + -
133B LEU* 3.7 35.4 - - + -
134B CYS 3.3 5.2 - - - +
135B LYS* 4.1 29.6 - - + +
136B GLU 4.5 0.4 - - - +
145B LEU* 6.5 0.7 - - + -
161B VAL* 3.7 20.4 - - + +
170B TRP* 2.7 57.9 - + + -
171B TRP* 1.3 79.0 - - - +
173B ARG* 1.3 64.7 + - - +
191B LEU* 3.5 4.5 - - - +
192B LEU* 2.7 42.3 + - + +
194B LEU* 4.0 13.0 - - + -
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Residues in contact with ARG 173 (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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104B LEU* 4.0 2.9 - - - -
133B LEU* 3.9 0.9 - - - +
134B CYS* 3.0 31.3 + - - +
136B GLU* 3.3 36.0 + - + +
172B TYR* 1.3 77.5 - - - +
174B CYS* 1.3 62.1 + - - +
175B TYR* 4.3 9.1 - - + -
188B PRO* 4.1 25.2 - - + +
189B SER* 3.7 25.4 + - - +
190B ASP* 4.3 1.7 - - - +
191B LEU* 3.9 41.3 - - + +
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Residues in contact with CYS 174 (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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102B PRO* 3.4 15.9 - - - +
103B THR 4.1 0.9 - - - -
104B LEU* 3.9 20.8 - - + +
122B CYS* 2.0 56.1 - - + -
132B SER 3.2 11.7 - - - +
133B LEU* 4.4 6.3 - - + -
173B ARG* 1.3 75.2 - - - +
175B TYR* 1.3 63.8 + - - +
188B PRO* 3.8 0.5 - - - +
189B SER* 2.8 39.8 + - - -
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Residues in contact with TYR 175 (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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15B VAL* 4.0 12.4 - - + +
17B THR* 6.1 0.3 - - - +
96B THR* 3.5 27.1 + - + +
102B PRO* 3.9 6.7 - - - -
122B CYS* 3.8 0.7 - - - -
131B PHE* 3.4 10.6 - - - -
132B SER* 2.9 33.3 + - - +
134B CYS* 3.8 22.4 - - + -
136B GLU* 4.8 3.1 + - - -
173B ARG* 4.3 15.1 - - + -
174B CYS* 1.3 79.0 - - - +
176B ALA* 1.3 60.7 + - - +
177B TYR* 5.5 0.4 - - + -
185B TRP* 3.5 40.6 - + + -
186B SER* 3.4 24.5 - - - +
187B LEU 3.9 0.2 - - - -
188B PRO* 3.3 38.2 - - + +
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Residues in contact with ALA 176 (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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99B TYR* 3.8 1.6 - - - -
100B ILE 5.2 0.9 - - - +
102B PRO* 4.3 6.5 - - + +
124B SER* 4.4 5.4 - - - +
128B PHE* 3.4 37.7 - - + -
130B GLY 3.6 5.4 - - - -
131B PHE* 4.0 13.5 - - + -
175B TYR* 1.3 74.4 - - - +
177B TYR* 1.3 63.4 + - - +
185B TRP* 3.9 0.5 - - - -
186B SER* 3.0 38.4 + - - +
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Residues in contact with TYR 177 (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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2A HIS* 3.3 34.6 + + - -
4A PRO* 4.0 5.5 - - - +
99B TYR* 4.3 2.7 - - - -
128B PHE* 3.6 19.2 - - - +
129B ASP 3.6 1.2 + - - -
130B GLY* 3.0 42.6 + - - +
131B PHE 3.7 20.6 - - - -
132B SER* 4.4 1.8 - - - -
146B ASN* 3.6 38.1 + - - +
147B SER 4.2 0.2 + - - -
176B ALA* 1.3 78.1 - - - +
178B ASP* 1.3 75.9 + - - +
179B SER* 4.2 2.9 - - - -
181B SER 4.8 0.4 - - - +
182B PRO* 4.1 15.5 - - + -
184B GLU 3.5 20.6 - - - +
185B TRP* 3.5 26.5 - + + -
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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