Contacts of the strand formed by residues 169 - 174 (chain C) in PDB entry 6V3O
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 THR 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ASN 4.0 2.4 + - - -
168C GLN* 1.3 81.9 + - - +
170C VAL* 1.3 74.2 + - - +
171C ASP* 4.8 4.9 - - + +
281C SER* 2.8 21.3 + - - +
282C LEU 3.5 6.3 - - - -
284C ARG* 4.5 20.9 - - + -
666C GLY 2.7 19.3 + - - +
667C SER* 3.6 4.0 + - - -
668C ILE 3.4 17.7 + - - +
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLN* 4.2 9.4 - - - +
169C THR* 1.3 78.1 - - - +
171C ASP* 1.3 63.0 + - - +
172C LEU* 3.8 25.4 - - + -
282C LEU 3.1 10.2 + - - +
283C ILE* 3.3 11.4 - - + +
284C ARG 2.8 26.0 + - - +
668C ILE* 3.6 17.7 - - + +
670C VAL* 5.5 2.5 - - + -
694C PHE* 4.0 30.3 - - + +
695C THR* 4.9 2.5 - - - +
698C THR* 3.6 30.1 - - + +
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Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C THR* 5.0 4.9 - - + -
170C VAL* 1.3 74.8 - - - +
172C LEU* 1.3 64.9 + - - +
173C VAL* 3.9 1.1 + - - +
284C ARG* 3.3 27.0 - - + +
285C PHE 3.7 0.2 + - - -
286C SER* 2.5 31.3 + - - -
668C ILE 3.1 7.1 + - - +
669C ARG* 2.9 39.2 + - + +
670C VAL 3.0 25.5 + - - +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.8 26.2 - - + -
171C ASP* 1.3 73.7 - - - +
173C VAL* 1.3 59.0 + - - +
174C PHE* 4.0 2.6 + - + -
283C ILE* 4.8 5.4 - - + -
284C ARG 2.9 8.1 + - - +
285C PHE* 3.3 36.3 - - + +
286C SER 2.9 23.6 + - - +
670C VAL* 3.5 10.3 - - + +
672C VAL* 3.7 14.4 - - + -
681C PHE* 3.9 20.2 - - + -
691C LEU* 4.5 10.5 - - + -
694C PHE* 4.1 38.8 - - + -
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP 4.0 8.1 - - - +
172C LEU* 1.3 75.6 - - - +
174C PHE* 1.3 65.2 + - - +
175C THR* 4.2 2.6 - - + +
286C SER* 3.6 15.9 - - - +
287C SER 4.2 0.2 - - - +
288C TRP* 3.5 37.2 - - + +
454C ASP* 4.0 4.7 - - - +
638C PHE* 3.6 28.7 - - + -
669C ARG* 3.8 21.3 - - - +
670C VAL 2.9 13.2 + - - +
671C THR* 3.4 5.5 - - - -
672C VAL* 2.7 30.3 + - - +
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Residues in contact with PHE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU 4.7 1.1 - - - -
173C VAL* 1.3 73.7 - - - +
175C THR* 1.3 61.5 + - - +
244C GLY* 5.1 7.4 - - - +
245C MET* 5.0 5.6 - - + -
247C TYR* 5.7 4.5 - - + -
248C ILE* 4.0 31.6 - - + -
252C VAL* 5.0 5.4 - - + -
285C PHE* 3.7 37.5 - + + -
286C SER 2.9 19.6 + - - +
287C SER* 3.6 2.9 + - - -
288C TRP* 3.1 25.6 + - - +
289C MET* 4.3 19.3 + - + +
451C VAL* 4.8 2.2 - - + -
672C VAL* 4.0 18.2 - - + -
677C ILE* 3.7 29.2 - - + -
681C PHE* 4.1 28.7 - + - -
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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