Contacts of the strand formed by residues 189 - 194 (chain A) in PDB entry 5VLR
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 ALA 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ARG* 1.4 75.9 - - - +
190A LEU* 1.3 60.2 + - - +
191A LEU 4.3 0.8 + - - -
206A GLN* 6.0 3.4 - - + -
207A VAL 4.4 2.0 - - - -
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Residues in contact with LEU 190 (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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188A ARG* 4.8 2.2 - - + +
189A ALA* 1.3 74.4 - - - +
191A LEU* 1.4 62.1 + - - +
192A VAL* 3.4 16.2 + - + +
206A GLN* 3.2 6.8 - - - +
207A VAL 3.0 38.9 + - - +
208A SER 5.7 0.2 - - - -
209A THR* 5.0 10.3 - - - +
262A ILE* 6.3 2.9 - - + -
266A LEU* 5.4 11.7 - - + -
272A PRO* 5.8 3.4 - - + -
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Residues in contact with LEU 191 (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 4.3 0.8 - - - -
190A LEU* 1.4 69.1 - - - +
192A VAL* 1.3 59.0 + - - +
193A ASN 4.2 0.2 - - - -
204A THR* 4.1 20.2 - - + -
205A PHE 4.2 0.4 - - - -
206A GLN* 4.0 14.9 - - + +
271A THR* 3.3 36.4 - - + +
272A PRO* 3.7 6.6 - - - +
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Residues in contact with VAL 192 (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 LEU* 3.7 18.2 - - + +
191A LEU* 1.3 76.8 - - - +
193A ASN* 1.3 58.0 + - - +
194A VAL* 3.3 19.6 + - + +
203A PHE 3.4 0.2 - - - +
204A THR* 3.3 2.4 - - - -
205A PHE* 2.8 45.8 + - - +
207A VAL* 5.5 4.5 - - + +
216A LEU* 5.9 7.0 - - + -
262A ILE* 6.1 2.7 - - + -
272A PRO* 3.4 36.3 - - + +
274A LEU* 4.6 15.3 - - + -
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Residues in contact with ASN 193 (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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191A LEU 4.2 1.0 + - - -
192A VAL* 1.3 66.6 - - - +
194A VAL* 1.3 61.4 + - - +
195A LYS* 4.9 6.1 - - - +
202A SER* 3.3 31.7 + - - -
204A THR* 3.2 27.9 + - + +
271A THR* 5.0 3.2 - - - +
272A PRO 3.0 9.3 + - - -
273A HIS* 3.3 47.2 + - + +
274A LEU 3.2 22.1 + - - +
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Residues in contact with VAL 194 (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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192A VAL* 3.8 20.2 - - + +
193A ASN* 1.3 79.0 - - - +
195A LYS* 1.4 78.5 + - - +
196A PHE* 5.1 2.9 - - + -
202A SER* 3.4 1.6 - - - -
203A PHE* 2.8 51.3 + - + +
205A PHE* 4.5 7.6 - - + -
216A LEU* 4.6 11.0 - - + +
220A ALA* 3.8 28.7 - - + -
274A LEU* 4.4 15.5 - - + +
275A THR 5.2 0.2 - - - +
276A MET* 4.6 12.8 - - + -
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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