Contacts of the strand formed by residues 205 - 213 (chain B) in PDB entry 5VGR
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 PHE 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B THR* 3.9 18.2 - - + +
165B MET* 3.5 39.7 - - + -
167B SER 6.0 0.4 - - - +
189B PHE* 3.5 44.4 - + + -
192B TYR* 3.9 26.2 - + - -
203B LYS 3.9 3.0 - - - +
204B PRO* 1.3 89.0 - - + +
206B GLN* 1.3 67.1 + - - +
256B CYS* 3.0 22.1 + - + +
257B PHE* 3.5 30.7 - + + -
258B SER* 3.0 27.5 + - - -
309B LYS* 5.0 6.1 - - - +
343B MET* 6.2 0.2 - - - -
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B SER 4.8 5.4 + - - +
168B SER* 3.3 19.2 - - - +
205B PHE* 1.3 76.5 - - - +
207B THR* 1.3 63.5 + - - +
257B PHE* 3.6 4.5 - - - +
258B SER* 2.9 34.3 + - - +
259B ASP* 3.0 10.7 + - - +
307B MET* 3.7 24.3 - - + +
308B GLU 3.3 16.9 + - - -
309B LYS* 3.1 19.6 - - - +
310B GLU* 2.6 47.6 + - + +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B SER 3.3 11.9 + - - +
169B VAL* 3.6 19.8 - - + -
170B GLN* 2.8 34.0 + - - +
206B GLN* 1.3 77.3 - - - +
208B LEU* 1.3 60.7 + - - +
209B MET* 4.3 4.9 - - + +
257B PHE* 4.2 3.6 - - - -
259B ASP* 3.5 23.2 + - + +
261B THR* 3.8 21.3 - - + +
307B MET* 3.3 21.7 - - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE* 5.1 2.0 - - + -
170B GLN* 3.4 32.8 - - + +
172B TYR* 4.1 19.3 - - + -
186B LEU* 3.9 15.7 - - + -
207B THR* 1.3 72.8 - - - +
209B MET* 1.3 60.9 + - - +
210B PHE* 3.5 34.8 - - + -
253B ILE* 4.2 6.1 - - + -
257B PHE* 3.6 45.4 - - + -
259B ASP 3.0 8.7 + - - +
260B VAL* 3.4 6.7 - - + +
261B THR* 2.9 27.9 + - - +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 4.7 12.6 - - + -
170B GLN 2.8 11.9 + - - +
171B ILE* 3.4 19.7 - - + +
172B TYR* 2.7 33.9 + - - -
207B THR* 4.1 7.4 - - + +
208B LEU* 1.3 71.8 - - - +
210B PHE* 1.3 69.1 + - - +
211B LEU* 3.4 3.7 + - - -
225B LEU* 6.1 0.2 - - - -
261B THR* 3.3 23.3 - - - +
262B CYS 4.4 1.8 - - - +
263B PHE* 4.2 12.8 - - + +
296B LEU* 4.1 22.2 - - - -
299B TYR* 3.7 32.3 - - + -
300B VAL* 4.1 14.6 - - + -
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B TYR* 3.5 28.9 - + + +
174B LEU* 3.7 20.4 - - + -
178B ILE* 4.0 22.9 - - + -
182B ASP* 5.7 0.2 - - + -
183B LEU* 3.9 23.3 - - + -
186B LEU* 3.9 13.9 - - + -
208B LEU* 3.5 30.5 - - + -
209B MET* 1.3 72.3 - - - +
211B LEU* 1.3 58.8 + - - +
212B VAL* 3.8 1.3 - - + -
232B LEU* 3.9 16.4 - - + -
253B ILE* 4.5 3.4 - - + -
260B VAL* 3.8 15.7 - - + -
261B THR 2.9 22.4 + - - +
262B CYS* 3.2 12.5 - - + -
263B PHE 2.8 29.1 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 5.8 0.7 - - + -
76B ILE* 4.3 21.8 - - + -
171B ILE* 3.8 30.3 - - + -
172B TYR 2.9 11.4 + - - +
173B ASN* 3.5 22.3 - - - +
174B LEU* 2.8 33.8 + - - +
209B MET* 3.4 3.4 + - - -
210B PHE* 1.3 70.5 - - - +
212B VAL* 1.3 57.4 + - - +
213B ARG* 3.7 11.8 + - - -
263B PHE* 3.6 28.3 - - + +
265B LEU* 4.2 11.4 - - + -
296B LEU* 3.9 30.3 - - + -
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LEU* 3.5 6.7 - - + +
176B GLN* 3.5 36.8 - - - +
177B ASN* 3.7 6.3 - - - +
178B ILE* 4.0 22.9 - - + +
210B PHE* 4.3 2.7 - - + +
211B LEU* 1.3 74.3 - - - +
213B ARG* 1.3 60.2 + - - +
215B TRP* 3.9 19.3 + - + +
231B PHE* 4.8 1.1 - - + -
262B CYS* 3.9 15.0 - - - -
263B PHE 3.0 5.9 + - - -
264B LEU* 3.5 22.8 - - + -
265B LEU* 2.8 33.5 + - - +
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS 3.5 12.0 + - - +
72B GLY* 2.9 30.8 + - - -
73B LYS* 4.4 0.2 - - - +
75B PHE* 4.3 6.5 - - - +
76B ILE* 3.5 21.4 - - - +
173B ASN* 2.9 32.0 + - - +
174B LEU 2.8 19.9 + - - +
175B SER* 3.8 5.6 - - - +
176B GLN* 2.7 29.1 + - - +
211B LEU* 4.1 8.7 - - - +
212B VAL* 1.3 70.0 - - - +
214B ASP* 1.3 76.9 + - - +
215B TRP 3.2 3.3 + - - -
265B LEU* 3.7 27.9 - - - +
289B PHE* 4.8 1.8 - - - -
501B GDP 2.9 49.0 + - + +
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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