Contacts of the strand formed by residues 161 - 167 (chain C) in PDB entry 1VEW
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 PHE 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C VAL* 3.3 2.2 - - - -
133C LEU* 2.8 44.5 + - + +
150C LEU* 4.5 13.0 - - + -
160C GLY* 1.3 71.2 - - - -
162C PRO* 1.3 79.2 - - + +
163C ILE* 3.5 14.6 + - + +
200C ARG* 3.4 55.9 - - + -
203C ALA* 5.7 0.2 - - + -
204C LYS* 3.6 24.9 - - - +
205C LYS* 3.5 37.2 - - + -
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Residues in contact with PRO 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.1 17.9 - - + -
130C TRP* 4.0 24.9 - - + -
131C LEU 3.8 5.2 - - - +
132C VAL* 4.0 4.9 - - + -
148C SER* 4.6 3.1 - - - +
149C PRO* 4.1 17.0 - - + -
150C LEU* 3.7 27.1 - - + -
160C GLY 3.6 4.9 - - - +
161C PHE* 1.3 97.3 - - + +
163C ILE* 1.3 62.2 + - - +
164C MET 4.8 0.9 - - - +
200C ARG* 2.8 33.7 + - - +
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Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 5.1 1.9 - - - +
98C LEU* 4.7 9.2 - - + -
131C LEU* 2.8 33.0 + - + +
132C VAL 4.3 2.0 - - - -
133C LEU* 4.2 18.2 - - + +
138C LEU* 4.4 10.8 - - + -
161C PHE* 3.8 31.9 - - + +
162C PRO* 1.3 74.8 - - - +
164C MET* 1.3 62.5 + - + +
197C ALA* 3.4 37.4 - - + +
200C ARG* 3.3 22.6 - - - +
201C PHE* 3.9 27.1 - - + +
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Residues in contact with MET 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.6 7.6 - - - -
87C GLY* 5.6 6.7 - - - +
112C PHE* 3.7 29.8 - - + -
116C PHE* 3.9 24.9 - - + -
130C TRP* 3.5 9.4 - - - -
131C LEU* 2.9 40.0 + - + +
162C PRO 3.6 0.6 - - - -
163C ILE* 1.3 86.9 - - + +
165C GLY* 1.3 62.3 + - - +
188C PHE* 4.2 12.8 - - + -
189C TRP* 4.8 5.2 - - + -
192C VAL* 4.1 20.2 - - + -
194C TRP* 4.1 20.0 - - + -
197C ALA* 4.6 7.9 - - + -
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.2 8.8 - - - +
84C PHE* 3.7 15.9 - - - -
116C PHE* 4.5 1.1 - - - -
128C TRP* 4.5 4.7 - - - -
129C ALA 3.2 11.2 - - - -
130C TRP* 3.8 16.4 - - - -
164C MET* 1.3 80.0 - - - +
166C LEU* 1.3 60.3 + - - +
188C PHE* 3.8 14.8 - - - -
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 4.6 0.2 - - + -
84C PHE* 4.0 5.6 - - + -
116C PHE* 3.9 24.2 - - + -
120C ALA* 4.3 4.3 - - + -
128C TRP* 3.3 8.6 - - - -
129C ALA* 2.9 30.6 + - + +
165C GLY* 1.3 74.8 - - - +
167C ASP* 1.3 67.3 + - - +
168C VAL* 3.5 17.2 + - + +
184C TYR* 3.4 32.1 - - + +
185C ILE* 4.1 23.6 - - + -
188C PHE* 3.5 44.9 - - + -
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 3.0 8.3 + - - -
81C HIS* 3.4 1.9 + - - -
84C PHE* 3.7 17.0 - - + -
128C TRP* 3.4 28.8 - - + -
166C LEU* 1.3 73.7 - - - +
168C VAL* 1.3 62.9 + - - +
169C TRP* 3.2 15.0 + - - -
172C ALA* 3.8 14.5 - - + +
184C TYR* 2.7 31.5 + - - -
206C MN 2.0 34.8 + - - -
207C OH 2.8 15.1 + - - -
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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