Contacts of the strand formed by residues 210 - 216 (chain A) in PDB entry 2VIG
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 ILE 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 5.9 4.0 - - + -
163A ALA 4.3 5.8 - - - +
164A GLY* 3.8 35.0 - - - +
166A ALA* 4.3 11.7 - - + +
198A PHE* 4.0 13.7 - - + -
199A ALA 3.4 18.8 - - - +
200A SER* 4.5 6.5 - - - -
201A THR* 3.8 0.7 - - - -
208A LYS 3.5 0.2 - - - -
209A SER* 1.3 91.8 - - - +
211A SER* 1.3 74.4 + - - +
258A GLY* 3.0 15.3 + - - -
260A GLY* 2.8 29.8 + - - -
261A PHE* 4.0 25.9 - - + +
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Residues in contact with SER 211 (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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198A PHE* 3.4 4.2 - - - -
199A ALA 2.9 31.2 + - - -
201A THR* 2.9 26.9 + - - +
210A ILE* 1.3 72.8 - - - +
212A ALA* 1.3 61.3 + - - +
213A PHE* 3.6 25.8 - - - -
253A ILE* 4.1 11.2 - - - +
256A GLU 4.8 1.1 - - - -
257A PRO* 3.3 9.3 - - - +
258A GLY 3.1 17.1 + - - +
260A GLY* 3.8 9.0 - - - +
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Residues in contact with ALA 212 (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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196A VAL* 4.6 5.4 - - + -
197A VAL 3.4 4.5 - - - +
198A PHE* 3.6 28.9 - - + -
211A SER* 1.3 73.8 - - - +
213A PHE* 1.3 61.6 + - - +
253A ILE* 3.4 10.8 - - - +
254A LEU* 2.8 47.3 + - + +
256A GLU 5.5 0.6 + - - -
260A GLY* 3.9 3.2 - - - +
263A ILE* 4.2 14.6 - - + +
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Residues in contact with PHE 213 (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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170A ALA* 3.5 31.2 - - + -
177A TRP* 3.5 36.8 - + + -
179A LEU* 4.7 4.5 - - + -
195A ALA 3.3 4.3 - - - +
196A VAL* 3.4 3.0 - - - +
197A VAL* 2.7 47.0 + - + +
199A ALA* 4.1 9.9 - - + -
201A THR* 3.7 6.3 - - + -
211A SER* 3.6 37.5 - - - -
212A ALA* 1.3 77.7 - - - +
214A LEU* 1.3 64.3 + - - +
215A VAL* 4.3 5.2 - - + -
248A ILE* 3.9 28.9 - - + -
252A SER 3.4 2.0 - - - -
253A ILE* 3.9 20.6 - - + -
254A LEU* 5.2 0.2 - - - -
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Residues in contact with LEU 214 (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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123A TYR* 5.1 0.2 - - + -
127A ILE* 3.9 22.2 - - + -
135A GLN* 4.1 27.6 - - + +
139A TRP* 3.6 58.8 - - + +
195A ALA 3.5 4.0 - - - +
196A VAL* 3.8 27.8 - - + -
213A PHE* 1.3 73.7 - - - +
215A VAL* 1.3 61.4 + - - +
216A PRO* 4.3 1.6 - - - +
248A ILE* 4.4 1.2 - - - +
252A SER* 2.7 38.0 + - - +
254A LEU* 4.4 15.3 - - + -
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Residues in contact with VAL 215 (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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139A TRP* 3.8 5.0 - - - -
179A LEU* 4.2 7.9 - - + -
194A ALA* 3.2 1.6 - - - -
195A ALA* 2.9 38.2 + - + +
197A VAL* 3.7 28.7 - - + -
213A PHE 4.0 4.7 - - - +
214A LEU* 1.3 77.3 - - - +
216A PRO* 1.3 81.9 - - + +
217A MET* 4.0 1.4 - - + +
219A THR* 3.8 16.2 - - + -
222A LEU* 4.4 5.4 - - + -
243A PHE* 4.1 15.5 - - + -
248A ILE* 4.0 26.9 - - + -
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Residues in contact with PRO 216 (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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139A TRP* 3.7 18.6 - - + -
193A SER 3.9 8.3 - - - +
194A ALA* 4.3 0.9 - - - -
214A LEU 4.3 1.8 - - - +
215A VAL* 1.3 95.0 - - + +
217A MET* 1.3 60.8 + - - +
218A PRO 3.5 8.2 - - - +
219A THR* 3.3 40.6 + - - +
222A LEU* 4.1 0.3 - - - +
248A ILE* 4.9 7.9 - - + -
249A PRO* 6.1 2.9 - - + -
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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