Contacts of the strand formed by residues 189 - 193 (chain A) in PDB entry 1V1A
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 LEU 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 4.7 9.4 - - + -
159A ARG* 4.9 6.3 - - - +
160A VAL 3.6 2.9 + - - +
161A SER* 3.7 8.8 + - - +
162A LEU 3.1 17.3 + - - -
187A VAL* 3.1 13.7 - - - +
188A ASP* 1.3 81.4 - - + +
190A LEU* 1.3 69.1 + - - +
191A PHE* 3.5 32.5 - - + -
215A GLU* 3.1 27.1 - - + +
217A VAL* 3.9 27.6 - - + -
257A TYR* 3.9 18.6 - - + -
258A LEU* 4.0 19.7 - - + -
261A ALA* 5.8 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
----------------------------------------------------------
162A LEU* 3.5 28.9 - - + +
164A VAL* 4.4 13.2 - - + -
180A LEU* 6.0 2.0 - - + -
184A LEU* 4.3 11.2 - - + -
187A VAL* 4.3 16.2 - - + -
189A LEU* 1.3 76.9 - - - +
191A PHE* 1.3 63.1 + - - +
192A LEU* 5.2 4.0 - - + -
211A LEU* 3.5 50.5 - - + +
213A ALA* 4.4 1.8 - - + -
215A GLU 2.9 6.8 + - - +
216A VAL* 3.3 22.5 - - + +
217A VAL* 2.6 35.3 + - - +
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 4.9 0.9 - + - -
161A SER* 3.1 26.9 - - - -
162A LEU 3.1 14.6 + - - -
163A ASP* 3.8 21.9 - - + +
164A VAL* 3.3 26.3 + - - +
189A LEU* 3.5 27.1 - - + -
190A LEU* 1.3 75.9 - - - +
192A LEU* 1.3 63.8 + - - +
217A VAL* 3.4 13.5 - - + +
219A LYS* 4.8 6.7 - - + -
253A PHE* 3.8 25.6 - + - -
254A ALA* 3.6 36.8 - - + -
257A TYR* 3.6 30.3 - + + -
258A LEU* 4.5 3.1 - - + -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 5.3 0.2 - - - -
164A VAL* 3.9 18.2 - - + -
190A LEU* 5.2 7.0 - - + -
191A PHE* 1.3 76.6 - - - +
193A SER* 1.3 60.3 + - - +
196A GLU* 3.6 31.4 - - + +
197A ALA* 3.4 32.1 - - + +
200A LEU* 5.7 1.1 - - + -
207A ALA* 4.2 12.3 - - + -
208A LEU* 5.2 10.3 - - + -
211A LEU* 4.3 15.3 - - + -
216A VAL* 5.5 4.0 - - + -
217A VAL 2.9 10.6 + - - +
218A LEU* 3.3 14.7 - - + +
219A LYS* 2.6 40.6 + - - +
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Residues in contact with SER 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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192A LEU* 1.3 77.3 - - - +
194A GLU* 1.3 68.6 + - - +
195A GLU* 2.6 13.4 + - - +
196A GLU* 2.7 40.5 + - - +
197A ALA 3.3 4.5 + - - -
218A LEU* 4.1 1.1 - - - -
219A LYS* 3.3 17.4 - - - +
1303A ADP 3.8 29.8 + - - -
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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