Contacts of the strand formed by residues 209 - 217 (chain A) in PDB entry 3VNG
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 GLN 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A GLY 3.2 6.3 - - - +
204A TYR* 3.6 22.0 - - + -
208A ASP* 1.3 96.9 + - - +
210A LEU* 1.4 60.8 + - - +
232A ARG* 3.0 26.7 + - + -
233A ARG 4.1 9.0 - - - +
234A SER* 3.5 18.3 + - - +
251A TYR* 3.1 40.2 - - - +
252A ASP* 3.1 31.5 - - - +
253A GLY* 3.3 11.8 + - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 3.6 19.3 - - + -
185A ILE 3.5 24.0 - - - +
186A ARG* 3.9 20.0 - - + +
202A GLY* 3.2 24.5 - - - +
203A GLY 2.7 20.9 + - - +
205A ASP* 3.3 27.8 - - + +
208A ASP* 3.8 9.9 - - + +
209A GLN* 1.4 78.3 - - - +
211A ASN* 1.4 59.9 + - - +
212A SER* 4.2 7.0 - - - +
229A MET* 3.9 0.7 - - - +
232A ARG* 3.8 11.7 - - - +
233A ARG 2.9 18.5 + - - -
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Residues in contact with ASN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 1.4 74.4 - - - +
212A SER* 1.3 72.1 + - - +
213A VAL* 3.8 1.7 - - - +
228A PRO* 3.1 11.4 - - - +
229A MET* 2.7 59.3 + - - +
230A LYS 4.6 5.5 + - - -
231A HIS 4.0 0.9 - - - -
232A ARG* 3.6 47.3 + - + +
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Residues in contact with SER 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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184A THR* 4.2 4.9 + - - +
186A ARG* 2.7 35.3 + - - -
202A GLY 3.0 24.1 + - - -
210A LEU* 3.6 7.2 - - - +
211A ASN* 1.3 87.8 + - - +
213A VAL* 1.3 60.6 + - - +
225A PHE* 4.0 16.8 - - - -
228A PRO* 3.9 9.0 - - - -
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Residues in contact with VAL 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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186A ARG* 4.2 1.6 - - - -
199A TYR* 4.3 15.5 - - + -
200A ALA 3.4 12.3 - - - +
201A ALA* 3.6 24.2 - - + -
211A ASN 3.8 9.2 + - - +
212A SER* 1.3 82.6 - - - +
214A GLU* 1.3 64.2 + - - +
225A PHE* 3.4 7.7 - - - -
226A VAL* 2.8 41.7 + - + +
227A ALA 3.6 19.7 - - - +
228A PRO* 4.3 3.6 - - - +
229A MET* 3.8 6.3 - - + -
270A TRP* 3.8 20.6 - - + -
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Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A MET* 3.3 9.9 - - - +
183A ASN* 2.7 38.5 + - - +
184A THR* 3.1 19.8 + - - -
186A ARG* 2.9 33.7 + - - +
198A ILE 3.9 0.3 - - - +
199A TYR* 3.4 3.1 - - - +
200A ALA* 2.9 36.9 + - + +
213A VAL* 1.3 78.2 - - - +
215A ARG* 1.3 61.0 + - - +
223A TRP* 3.3 18.9 - - + +
224A THR 3.3 16.6 - - - +
225A PHE* 4.2 7.2 - - + +
226A VAL* 4.3 0.7 - - - +
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Residues in contact with ARG 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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197A CYS* 3.5 34.1 - - + -
198A ILE 3.3 6.1 - - - +
199A TYR* 3.0 39.9 + - + -
214A GLU* 1.3 76.9 - - - +
216A TYR* 1.3 62.9 + - - +
217A ASP* 3.9 2.5 + - + +
222A THR 3.4 1.9 - - - +
223A TRP* 3.3 5.7 - - - -
224A THR* 2.7 49.4 + - - +
225A PHE 5.7 0.2 + - - -
226A VAL* 3.7 27.5 - - + +
263A TYR* 4.2 8.3 + - - -
265A PRO* 5.0 7.7 + - - +
268A ASP* 6.4 0.2 - - - -
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Residues in contact with TYR 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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147A LEU* 5.2 0.7 - - - +
152A TYR* 4.2 14.6 - + - -
179A ILE* 4.0 34.7 - - + +
180A THR* 4.2 7.7 + - - -
197A CYS* 3.5 10.4 - - - +
198A ILE* 2.7 38.8 + - + +
215A ARG* 1.3 73.7 - - - +
217A ASP* 1.3 59.9 + - - +
218A VAL* 3.8 30.6 + - + -
221A GLU* 3.4 46.9 - - - +
222A THR 3.3 13.5 - - - -
223A TRP* 3.5 45.6 - + + -
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Residues in contact with ASP 217 (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 ASN 5.3 0.5 - - - +
197A CYS* 4.0 19.7 - - - -
215A ARG* 3.9 2.4 + - + +
216A TYR* 1.3 74.1 - - - +
218A VAL* 1.3 54.5 + - - +
219A GLU* 3.0 26.0 - - - +
220A THR* 2.8 47.0 + - - +
221A GLU* 2.7 35.9 + - - -
222A THR* 3.0 10.6 + - - +
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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