Contacts of the strand formed by residues 161 - 166 (chain C) in PDB entry 2VRF
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 ASP 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG* 2.6 45.1 + - - -
141C LEU* 3.3 3.0 - - - -
142C ILE* 2.8 43.8 + - + +
157C LEU* 3.5 9.0 - - - +
158C ARG* 2.7 33.0 + - - +
159C LEU 3.3 0.6 + - - -
160C GLY* 1.3 77.1 - - - +
162C ALA* 1.3 59.9 + - - +
163C ILE 3.8 0.3 + - - -
194C VAL* 4.2 13.2 - - + -
195C LYS 3.6 2.2 - - - -
196C PHE* 3.5 17.4 + - - +
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Residues in contact with ALA 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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139C PRO* 4.3 9.4 - - + -
140C ILE 3.2 11.0 - - - +
141C LEU* 3.9 3.4 - - + -
160C GLY 3.6 1.8 + - - -
161C ASP* 1.3 72.3 - - - +
163C ILE* 1.3 61.1 + - - +
164C LEU* 3.6 13.6 + - + +
194C VAL* 3.1 7.6 - - - +
195C LYS* 2.7 43.1 + - + +
197C ILE* 3.7 25.6 - - + -
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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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128C ILE* 4.2 10.1 - - + -
130C ILE* 3.8 29.2 - - + -
139C PRO* 5.8 0.7 - - - +
140C ILE* 2.8 35.4 + - + +
142C ILE* 3.9 23.8 - - + +
162C ALA* 1.3 71.5 - - - +
164C LEU* 1.3 63.0 + - - +
165C SER 3.7 15.9 - - - +
171C LEU* 3.6 36.0 - - + +
172C ARG* 5.4 0.2 - - - -
183C LEU* 4.2 10.1 - - + -
192C LEU* 4.1 17.9 - - + -
193C GLU 3.6 4.9 - - - +
194C VAL* 4.2 10.3 - - + -
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Residues in contact with LEU 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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113C VAL* 4.5 7.2 - - + -
139C PRO* 6.0 3.8 - - + -
162C ALA* 4.3 18.4 - - + +
163C ILE* 1.3 76.4 - - - +
165C SER* 1.3 54.2 + - - +
170C ASP* 3.2 10.0 - - - +
171C LEU* 2.8 27.1 + - - -
172C ARG* 3.3 41.4 + - + +
193C GLU* 2.7 38.0 + - + +
194C VAL 4.5 1.6 - - - -
195C LYS* 3.9 36.6 - - + -
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Residues in contact with SER 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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163C ILE* 3.5 10.1 - - - +
164C LEU* 1.3 80.4 - - - +
166C VAL* 1.3 62.2 + - - +
168C GLY 5.0 1.6 - - - -
169C THR 3.1 18.4 - - - -
170C ASP* 4.1 3.6 - - - -
171C LEU* 4.1 3.6 - - - +
172C ARG* 4.2 3.8 - - - -
192C LEU* 3.5 4.2 - - - -
193C GLU* 2.7 55.2 + - - +
1205C EDO 3.1 17.4 + - - -
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Residues in contact with VAL 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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165C SER* 1.3 75.3 - - - +
167C ASN* 1.3 71.9 + - + +
168C GLY 3.2 1.3 - - - -
169C THR* 2.8 28.2 + - - +
171C LEU* 3.9 18.2 - - + -
182C ALA* 4.2 25.1 - - + +
183C LEU* 3.8 19.5 - - + -
186C ALA* 3.6 25.9 - - + +
190C VAL* 3.9 12.6 - - + -
191C LEU 3.5 3.6 - - - -
192C LEU* 3.8 17.3 - - + -
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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