Contacts of the strand formed by residues 180 - 183 (chain T) in PDB entry 1V2J
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 MET 180 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98T THR 3.5 19.1 - - - +
99T LEU 3.5 26.0 - - - +
100T ASN* 3.8 1.1 - - - -
101T ASN 6.0 0.2 - - - +
165T ASP* 5.2 0.7 - - - +
168T CYS* 5.4 0.9 - - - -
174T ARG 4.7 2.2 - - - +
175T ILE* 3.8 14.8 - - + -
176T ILE* 2.9 48.2 + - + +
177T THR* 3.3 27.1 - - - +
178T SER 3.7 0.2 - - - -
179T ASN* 1.3 86.3 - - + +
181T PHE* 1.3 66.3 + - - +
214T SER* 5.7 1.1 - - - +
215T TRP* 3.6 24.0 - - + +
227T VAL* 3.8 13.0 - - + -
228T TYR 3.1 12.6 - - - +
229T THR* 5.3 0.4 - - - -
230T LYS* 3.9 4.1 - - - +
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Residues in contact with PHE 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T ILE* 4.0 36.3 - - + -
163T LEU 5.8 0.7 - - - +
165T ASP* 5.4 7.4 - - - +
168T CYS* 3.9 9.6 - - - -
180T MET* 1.3 76.5 - - - +
182T CYS* 1.3 70.6 + - - +
183T ALA* 4.1 13.2 - - + -
199T VAL* 4.0 14.6 - - + -
210T GLN* 3.2 26.5 - - + -
211T GLY* 3.7 15.9 - - - -
227T VAL* 3.5 3.4 - - - -
228T TYR* 2.8 51.9 + + + -
229T THR 3.7 4.7 - - - -
230T LYS* 3.9 27.8 - - + +
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Residues in contact with CYS 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T ILE* 3.6 1.7 - - - +
163T LEU* 2.9 32.8 + - + +
168T CYS* 2.0 63.7 - - + +
171T ALA* 5.1 1.1 - - - -
175T ILE* 5.2 1.3 - - - -
181T PHE* 1.3 83.1 - - - +
183T ALA* 1.3 63.1 + - - +
225T PRO* 4.1 23.6 - - + -
226T GLY 3.3 11.7 - - - +
227T VAL* 4.6 12.6 - - - -
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Residues in contact with ALA 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T CYS* 6.1 1.1 - - + -
138T ILE* 4.9 3.8 - - + -
160T ALA* 4.7 9.9 - - + +
161T PRO 3.1 17.0 - - - +
162T ILE* 4.1 4.7 - - + -
163T LEU* 4.1 5.8 - - - -
181T PHE* 4.1 13.5 - - + -
182T CYS* 1.3 78.1 - - - +
184T GLY* 1.3 59.7 + - - +
189T ASP* 4.9 0.9 - - - +
199T VAL* 5.6 3.1 - - + -
225T PRO* 3.8 2.2 - - - +
226T GLY* 3.3 26.5 + - - +
228T TYR* 3.7 25.0 + - + -
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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