Contacts of the strand formed by residues 192 - 200 (chain P) in PDB entry 1VF5
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 ASN 192 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P ASP* 2.7 31.5 - - - +
189P GLU 3.2 6.8 + - - +
190P TYR 2.6 10.4 + - - +
191P GLY* 1.3 78.1 + - - +
193P VAL* 1.3 88.8 + - - +
194P LYS* 3.3 32.7 + - - +
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Residues in contact with VAL 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64P ASP 5.8 1.3 - - - +
187P GLU* 3.4 30.5 - - + +
188P ASP* 3.1 13.2 - - + +
189P GLU* 4.2 4.3 - - - +
190P TYR 4.6 6.1 - - - +
192P ASN* 1.3 93.1 + - - +
194P LYS* 1.3 60.2 + - - +
195P TYR* 3.3 35.8 - - + +
213P ALA* 3.3 14.4 - - + +
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Residues in contact with LYS 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P GLU* 2.6 29.4 - - - +
187P GLU 2.9 11.9 + - - +
188P ASP* 3.8 6.0 - - - +
192P ASN* 3.3 25.3 + - - +
193P VAL* 1.3 75.1 + - - +
195P TYR* 1.3 56.7 + - - +
196P GLN* 3.3 26.0 - - + +
210P THR* 4.0 6.3 - - - +
211P ILE 3.5 6.7 - - - +
212P PRO* 3.3 42.1 - - + +
213P ALA* 3.8 7.0 - - - +
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Residues in contact with TYR 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ALA 3.6 2.2 - - - -
185P LYS* 3.1 60.0 - - + +
186P GLU 3.8 10.3 - - - -
187P GLU* 5.2 2.2 - - - +
193P VAL* 3.3 36.3 - - + +
194P LYS* 1.3 77.9 - - - +
196P GLN* 1.3 71.5 - - - +
197P VAL* 3.9 0.2 - - - +
211P ILE* 3.2 31.7 + - + +
212P PRO 4.2 1.7 - - - +
213P ALA* 3.7 22.4 - - + -
214P GLY 5.5 0.2 - - - -
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Residues in contact with GLN 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ALA* 2.8 32.2 + - + +
185P LYS* 3.7 3.6 + - - +
186P GLU* 3.6 21.6 + - - +
194P LYS* 3.3 30.3 - - - +
195P TYR* 1.3 89.5 - - - +
197P VAL* 1.3 69.8 + - - +
209P ASP 3.6 4.1 - - - +
210P THR* 2.6 39.3 + - - -
211P ILE 4.2 4.0 - - - +
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Residues in contact with VAL 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ILE* 3.7 16.6 - - + -
182P LYS 4.5 0.9 - - - +
183P ILE* 5.6 1.3 - - - -
184P ALA* 3.3 9.5 - - - +
195P TYR 3.9 0.4 - - - +
196P GLN* 1.3 85.3 - - - +
198P SER* 1.3 76.1 + - - +
199P ILE* 3.6 27.6 - - + -
208P VAL* 3.5 11.9 - - - +
209P ASP* 3.1 27.5 + - + +
210P THR 4.6 1.3 - - - +
211P ILE* 3.8 34.1 - - + +
217P LEU* 5.9 5.4 - - + -
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Residues in contact with SER 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ILE* 3.7 6.9 - - - +
182P LYS* 3.3 33.9 + - - +
184P ALA* 2.7 32.5 - - - +
197P VAL* 1.3 78.5 + - - +
199P ILE* 1.3 54.9 + - - +
200P GLN* 2.4 31.0 - - - +
208P VAL* 3.6 10.1 - - - -
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Residues in contact with ILE 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P ALA* 3.9 26.5 - - + -
175P SER 4.1 1.8 - - - +
176P ALA* 4.9 10.3 - - + +
178P GLY 5.1 2.7 - - - +
180P ILE* 3.7 22.4 - - + +
197P VAL* 3.6 19.7 - - + +
198P SER* 1.3 75.1 - - - +
200P GLN* 1.3 72.3 + - - +
201P THR* 3.6 18.2 - - - +
206P THR* 4.7 0.9 + - - -
207P VAL* 2.7 25.5 - - + +
208P VAL* 2.8 24.4 - - - +
209P ASP* 3.0 34.3 - - + +
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Residues in contact with GLN 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P THR* 3.2 14.1 - - + +
180P ILE* 3.9 3.0 - - - +
181P THR* 2.6 47.3 + - + -
182P LYS* 4.0 8.5 - - - +
198P SER* 2.4 29.0 + - - +
199P ILE* 1.3 82.8 + - - +
201P THR* 1.3 73.0 + - - +
202P ASP* 2.8 16.6 + - + +
206P THR* 3.1 12.4 + - - +
207P VAL 3.0 22.9 + - - +
208P VAL* 4.9 2.8 - - - +
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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