Contacts of the strand formed by residues 205 - 208 (chain A) in PDB entry 2VWJ
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.4 7.6 - - + -
136A LYS 3.1 1.8 + - - -
137A MET* 3.4 25.7 - - + -
138A LEU 2.8 27.9 + - - -
203A PRO* 3.5 6.2 - - - +
204A ASP* 1.3 88.4 - - + +
206A LEU* 1.3 63.7 + - - +
207A ILE* 3.7 15.5 - - + -
256A ILE* 3.3 17.5 - - + +
258A PHE* 3.7 24.5 - - + -
327A PHE* 3.6 33.7 - - + -
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Residues in contact with LEU 206 (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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138A LEU* 3.3 17.7 - - + +
140A PHE* 4.0 27.8 - - + -
194A PHE* 5.3 0.2 - - + -
198A VAL* 4.3 17.0 - - + -
203A PRO* 4.0 22.4 - - + -
204A ASP 4.2 0.4 - - - -
205A VAL* 1.3 73.7 - - - +
207A ILE* 1.3 57.1 + - - +
216A PHE* 4.6 8.1 - - + -
232A LEU* 4.7 7.4 - - + -
252A VAL* 4.1 25.6 - - + -
255A ARG* 4.0 22.2 - - + +
256A ILE 2.9 8.9 + - - +
257A HIS* 3.5 11.6 - - + -
258A PHE 2.8 31.9 + - - -
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Residues in contact with ILE 207 (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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137A MET* 3.2 35.2 - - + -
138A LEU 2.7 19.0 + - - +
139A ALA* 3.3 5.5 - - + +
140A PHE 3.1 25.0 + - - +
205A VAL* 3.7 19.5 - - + +
206A LEU* 1.3 72.0 - - - +
208A THR* 1.3 64.6 + - - +
258A PHE* 3.4 14.1 - - + +
260A LEU* 3.7 20.9 - - + -
319A THR* 3.6 24.4 - - + +
320A TYR* 4.2 20.0 - - + +
323A GLY* 4.1 13.9 - - - -
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Residues in contact with THR 208 (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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140A PHE* 3.5 46.7 - - + +
207A ILE* 1.3 75.4 - - - +
209A TYR* 1.3 61.4 + - - +
210A ASN 3.9 0.2 - - - -
211A GLY* 3.2 21.6 + - - -
215A ALA* 5.4 2.5 - - + -
216A PHE* 3.8 4.5 - - + -
257A HIS* 2.4 36.6 + - + +
258A PHE 3.0 5.1 + - - +
259A ASP* 3.7 4.7 - - - -
260A LEU* 3.0 30.7 + - - +
319A THR* 3.8 6.3 - - - -
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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