Contacts of the strand formed by residues 169 - 175 (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 VAL 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B VAL* 5.6 1.6 - - + -
62B VAL 3.1 6.6 + - - +
63B VAL* 4.5 16.8 - - + -
64B SER* 2.9 31.7 + - - +
167B SER* 3.9 3.1 + - - -
168B SER* 1.3 88.8 - - - +
170B GLN* 1.3 59.8 + - - +
171B ILE* 3.8 25.8 - - + -
207B THR* 3.6 21.3 - - + -
209B MET* 4.7 10.1 - - + -
300B VAL* 4.7 11.0 - - + +
307B MET* 4.4 19.5 - - + +
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Residues in contact with GLN 170 (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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64B SER* 2.8 22.6 + - - +
66B ALA* 3.3 13.6 - - - +
160B PHE* 3.5 18.0 - - + -
163B SER* 3.0 22.6 + - - -
164B THR* 2.8 41.4 + - + +
167B SER* 3.9 8.9 + - - +
169B VAL* 1.3 71.1 - - - +
171B ILE* 1.3 62.4 + - - +
172B TYR* 3.5 3.5 + - + +
207B THR 2.8 15.9 + - - +
208B LEU* 3.4 22.7 - - + +
209B MET 2.8 30.5 + - - -
257B PHE* 5.0 1.3 - - + -
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Residues in contact with ILE 171 (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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63B VAL* 4.1 11.9 - - + -
64B SER 2.8 18.4 + - - +
65B VAL* 3.6 13.8 - - + +
66B ALA 2.9 26.6 + - - -
80B MET* 3.6 31.4 - - + -
169B VAL* 3.8 17.3 - - + +
170B GLN* 1.3 73.6 + - - +
172B TYR* 1.3 57.2 + - - +
173B ASN* 3.2 4.8 + - - +
209B MET* 3.4 18.8 - - + +
211B LEU* 3.8 36.6 - - + -
296B LEU* 5.7 2.0 - - + -
300B VAL* 4.3 15.7 - - + -
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Residues in contact with TYR 172 (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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66B ALA* 3.8 9.9 - - - -
67B GLY* 5.0 0.9 - - - -
147B PHE* 4.0 25.5 - + + +
160B PHE* 4.3 25.6 - + + -
170B GLN* 3.5 2.5 + - + -
171B ILE* 1.3 67.8 - - - +
173B ASN* 1.3 65.4 + - - +
174B LEU* 3.4 27.6 + - + +
182B ASP* 3.0 38.2 + - + +
185B GLN* 3.9 17.3 + - - +
186B LEU* 4.6 7.9 - - + -
208B LEU* 4.1 17.3 - - + -
209B MET 2.7 13.7 + - - +
210B PHE* 3.5 36.9 - + + -
211B LEU 2.9 22.7 + - - -
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Residues in contact with ASN 173 (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* 4.2 11.5 - - + +
66B ALA 2.7 22.7 + - - +
67B GLY* 3.9 9.7 - - - -
68B ALA 4.7 1.9 + - - -
71B LYS* 3.0 37.4 + - - +
73B LYS* 3.6 25.3 - - + +
76B ILE* 5.1 0.2 - - - +
171B ILE 3.2 1.9 + - - +
172B TYR* 1.3 68.3 - - - +
174B LEU* 1.3 67.9 + - - +
211B LEU* 3.5 22.2 - - + +
213B ARG* 2.9 30.2 + - - +
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Residues in contact with LEU 174 (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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67B GLY* 6.0 0.2 - - - -
71B LYS* 5.7 2.7 - - - -
172B TYR* 3.5 37.5 - - + +
173B ASN* 1.3 81.1 - - - +
175B SER* 1.3 55.7 + - - +
176B GLN 3.9 0.2 - - - -
177B ASN 3.8 11.2 - - - +
178B ILE* 3.8 19.3 - - + -
182B ASP* 3.8 35.0 - - + +
210B PHE* 3.7 30.3 - - + -
211B LEU 2.8 11.4 + - - +
212B VAL* 3.5 4.6 - - + -
213B ARG* 2.8 37.5 + - - +
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Residues in contact with SER 175 (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* 3.9 38.2 + - - +
174B LEU* 1.3 71.0 - - - +
176B GLN* 1.3 68.6 + - - +
177B ASN* 2.7 24.0 + - - +
179B GLN* 5.6 3.5 + - - -
213B ARG* 4.0 7.5 - - - +
214B ASP* 4.5 8.8 + - - -
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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