Contacts of the strand formed by residues 197 - 204 (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 CYS 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.4 1.8 - - - -
193A VAL* 3.3 5.0 - - - +
194A LEU 2.9 35.0 + - - +
195A HIS 3.2 5.4 - - - -
196A ASN* 1.4 87.1 - - - +
198A ILE* 1.3 64.7 + - - +
199A TYR* 3.6 3.0 - - + +
215A ARG* 3.5 36.3 - - + -
216A TYR 3.5 13.5 - - - +
217A ASP* 4.0 21.3 - - - -
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Residues in contact with ILE 198 (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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145A ALA* 3.4 25.6 - - + -
147A LEU* 3.8 36.1 - - + -
152A TYR* 4.1 22.2 - - + -
154A VAL* 4.7 6.1 - - + -
191A VAL* 3.9 20.6 - - + -
192A CYS 3.4 6.1 - - - +
193A VAL* 4.2 6.3 - - + -
197A CYS* 1.3 74.3 - - - +
199A TYR* 1.3 64.7 + - - +
214A GLU 3.9 0.2 - - - +
215A ARG* 3.3 4.0 - - - -
216A TYR* 2.7 50.7 + - + -
223A TRP* 3.9 16.9 - - + -
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Residues in contact with TYR 199 (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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190A GLY 4.2 0.9 - - - +
191A VAL* 3.2 10.4 - - - +
192A CYS* 2.8 45.1 + - - +
194A LEU* 3.6 42.8 + - + +
195A HIS* 5.6 1.4 - - - +
197A CYS* 3.6 11.6 - - - +
198A ILE* 1.3 77.0 - - - +
200A ALA* 1.3 61.3 + - - +
201A ALA* 4.1 1.6 - - + +
213A VAL* 4.3 20.2 - - + -
214A GLU 3.4 3.4 - - - -
215A ARG* 3.0 52.0 + - + -
223A TRP* 4.7 0.2 - - - -
226A VAL* 4.5 3.8 - - + -
238A ILE* 5.7 1.8 - - + -
245A ILE* 5.0 6.3 - - + -
263A TYR* 3.6 36.3 - + - -
265A PRO* 4.1 9.9 - - - +
270A TRP* 6.2 0.9 - + - -
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Residues in contact with ALA 200 (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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182A MET* 3.6 30.3 - - - -
186A ARG* 4.0 13.7 - - - -
189A ALA* 5.1 0.9 - - + -
190A GLY 3.4 4.5 - - - -
191A VAL* 4.1 13.5 - - + -
199A TYR* 1.3 74.1 - - - +
201A ALA* 1.3 60.9 + - - +
213A VAL* 3.4 3.3 - - - -
214A GLU* 2.9 33.0 + - + +
223A TRP* 3.9 13.0 - - + -
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Residues in contact with ALA 201 (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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189A ALA* 3.6 0.6 - - - +
190A GLY 2.7 42.6 + - - +
199A TYR* 5.6 1.6 - - + -
200A ALA* 1.3 73.0 - - - +
202A GLY* 1.3 65.7 + - - +
213A VAL* 3.6 26.9 - - + -
229A MET* 4.2 14.4 - - - -
236A LEU* 3.6 5.7 - - + +
238A ILE* 4.5 13.0 - - + -
245A ILE* 6.2 0.2 - - + -
247A VAL* 4.7 2.5 - - + -
270A TRP* 4.6 7.2 - - + -
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Residues in contact with GLY 202 (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* 2.8 25.3 + - - +
189A ALA* 3.4 9.1 - - - +
201A ALA* 1.3 75.5 - - - +
203A GLY* 1.3 61.0 + - - -
210A LEU* 3.2 24.2 - - - -
212A SER 3.0 17.7 + - - -
229A MET* 3.6 9.5 - - - +
233A ARG 3.5 5.2 - - - -
236A LEU* 4.6 0.2 - - - -
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Residues in contact with GLY 203 (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* 4.7 0.9 - - - -
187A SER 3.5 10.5 - - - -
188A GLY 3.6 13.9 - - - -
189A ALA* 3.7 6.8 - - - +
201A ALA 3.7 1.0 + - - -
202A GLY* 1.3 74.6 - - - -
204A TYR* 1.3 58.1 + - - -
209A GLN* 3.2 5.5 - - - -
210A LEU* 2.7 33.8 + - - -
233A ARG 2.7 11.8 + - - +
234A SER* 3.5 7.8 - - - +
236A LEU* 4.3 0.2 - - - +
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Residues in contact with TYR 204 (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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162A ARG* 3.3 40.2 + - - -
185A ILE* 4.1 3.2 - - - +
186A ARG* 3.7 1.4 + - - -
187A SER* 2.9 45.3 + - - +
203A GLY* 1.3 75.2 - - - +
205A ASP* 1.3 59.1 + - - +
206A GLY* 3.1 29.3 + - - -
207A GLN* 3.7 4.0 + - - -
208A ASP* 3.4 38.6 - - - -
209A GLN* 3.6 20.6 - - - -
210A LEU* 4.3 1.1 - - - +
234A SER* 4.2 11.2 - - - +
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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