Contacts of the strand formed by residues 189 - 196 (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 GLU 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C ARG* 3.5 36.3 + - + +
118C VAL 3.5 8.7 - - - +
119C VAL* 3.4 20.7 - - + +
167C ASN* 3.1 18.4 + - - +
186C ALA 4.0 2.4 - - - +
187C GLY* 4.8 0.3 - - - -
188C LYS* 1.3 79.9 - - + +
190C VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 190 (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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116C VAL 3.6 0.3 - - - +
117C ARG* 3.5 5.6 - - - +
118C VAL* 2.8 44.9 + - + +
120C LYS* 4.0 13.7 - - + -
126C LEU* 3.4 27.1 - - + -
166C VAL* 3.9 14.1 - - + -
167C ASN* 3.6 3.6 - - - -
183C LEU 4.8 1.1 - - - +
186C ALA* 3.5 28.3 - - + -
187C GLY 3.9 10.8 - - - +
189C GLU* 1.3 82.1 - - - +
191C LEU* 1.3 59.4 + - - +
192C LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 191 (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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115C ARG* 4.2 18.8 - - + +
116C VAL 3.5 28.0 - - - +
117C ARG* 4.1 9.6 - - + +
166C VAL* 3.5 1.7 - - - -
167C ASN* 2.9 37.2 + - - +
190C VAL* 1.3 71.8 - - - +
192C LEU* 1.3 60.4 + - - +
1205C EDO 3.1 32.4 - - - +
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Residues in contact with LEU 192 (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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114C ARG 3.5 1.4 - - - +
115C ARG* 3.3 4.8 - - - -
116C VAL* 2.8 41.1 + - + +
118C VAL* 4.0 15.5 - - + -
126C LEU* 4.9 8.1 - - + -
128C ILE* 5.5 2.2 - - + -
142C ILE* 5.8 0.2 - - + -
157C LEU* 4.0 30.3 - - + -
163C ILE* 4.1 16.6 - - + -
165C SER 3.5 1.3 - - - +
166C VAL* 3.8 19.3 - - + -
183C LEU* 3.7 29.6 - - + -
190C VAL* 3.8 14.6 - - + -
191C LEU* 1.3 72.2 - - - +
193C GLU* 1.3 60.5 + - - +
194C VAL* 3.8 14.5 + - + -
1205C EDO 4.6 2.0 - - - -
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Residues in contact with GLU 193 (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* 3.3 30.3 - - + +
114C ARG 3.5 3.1 - - - -
115C ARG* 4.4 16.7 + - + -
163C ILE* 3.6 1.2 - - - -
164C LEU* 2.7 41.4 + - + +
165C SER* 2.7 42.6 + - - +
172C ARG* 2.7 33.7 + - - -
191C LEU 4.1 0.6 + - - -
192C LEU* 1.3 72.4 - - - +
194C VAL* 1.3 55.8 + - - +
1205C EDO 4.2 11.6 + - - +
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Residues in contact with VAL 194 (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* 3.5 4.3 - - - +
114C ARG* 2.9 73.5 + - + +
116C VAL* 4.0 12.8 - - + -
142C ILE* 4.9 0.2 - - + -
157C LEU* 3.9 18.2 - - + -
161C ASP* 4.0 11.0 - - + +
162C ALA 3.1 12.8 - - - +
163C ILE* 4.2 14.4 - - + -
164C LEU* 4.5 3.1 - - - +
192C LEU* 4.1 15.5 - - + -
193C GLU* 1.3 79.6 - - - +
195C LYS* 1.3 61.3 + - - +
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Residues in contact with LYS 195 (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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-1C SER* 4.8 9.1 - - - +
0C MET* 3.2 36.8 + - + +
112C PRO 4.2 5.2 - - - +
113C VAL* 4.9 5.4 - - + +
114C ARG* 4.6 0.4 - - - +
161C ASP* 4.0 2.5 - - - -
162C ALA* 2.7 42.5 + - + +
164C LEU* 3.9 30.1 - - + -
194C VAL* 1.3 75.8 - - - +
196C PHE* 1.3 71.3 + - - +
197C ILE* 4.1 5.8 - - + +
135D GLU 4.9 9.3 + - - -
136D ASN* 6.2 0.2 - - - +
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Residues in contact with PHE 196 (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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0C MET* 3.0 52.7 - - + +
112C PRO 4.7 0.8 + - - -
114C ARG* 3.7 5.3 - - - +
158C ARG* 3.5 39.5 - - + +
159C LEU 3.5 22.4 - - - -
160C GLY* 4.1 6.3 - - - -
161C ASP* 3.5 20.8 + - - +
195C LYS* 1.3 76.9 - - - +
197C ILE* 1.3 84.0 + - - +
198C ARG* 3.9 15.0 - - + -
199C GLU 5.6 1.1 - - - -
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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