Contacts of the strand formed by residues 3164 - 3168 (chain C) in PDB entry 2H7C
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 VAL3164 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121C ILE* 4.0 15.5 - - + -
3122C TYR 3.5 10.8 - - - +
3123C THR* 3.7 22.0 - - - +
3124C PRO* 4.2 0.4 - - + -
3133C LEU* 4.2 13.0 - - + +
3134C PRO 3.0 10.0 + - - +
3135C VAL* 3.5 8.0 - - + +
3136C MET* 2.9 26.7 + - - +
3163C VAL* 1.3 73.2 - - - +
3165C VAL* 1.3 62.1 + - - +
3166C VAL* 4.3 3.8 - - + -
3205C ILE* 3.9 26.5 - - + -
3208C PHE 3.9 4.0 - - - +
3209C GLY 4.1 4.7 - - - +
3210C GLY* 3.9 23.6 - - - +
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Residues in contact with VAL3165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3121C ILE* 3.5 2.4 - - - +
3122C TYR* 2.8 52.1 + - + +
3136C MET* 3.5 9.6 - - + +
3154C GLY* 4.0 19.7 - - - +
3157C LEU* 4.0 14.4 - - + -
3158C ALA* 3.9 18.8 - - + +
3163C VAL* 3.9 22.0 - - + +
3164C VAL* 1.3 77.0 - - - +
3166C VAL* 1.3 70.1 + - - +
3167C THR* 4.3 11.2 - - + -
3218C PHE* 5.0 5.2 - - + -
3476C PHE* 4.7 12.1 - - + -
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Residues in contact with VAL3166 (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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3119C LEU* 4.2 20.9 - - + -
3120C ASN 3.3 9.6 - - - +
3121C ILE* 4.2 9.4 - - + -
3135C VAL* 4.0 14.8 - - + -
3136C MET 2.9 11.8 + - - +
3137C VAL* 3.3 11.8 - - + +
3138C TRP* 2.7 32.9 + - - +
3164C VAL* 4.3 2.7 - - + -
3165C VAL* 1.3 79.6 - - - +
3167C THR* 1.3 58.8 + - - +
3168C ILE* 4.0 20.0 - - + -
3201C VAL* 4.5 9.2 - - + -
3205C ILE* 3.9 27.4 - - + -
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Residues in contact with THR3167 (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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3119C LEU* 3.1 4.2 - - - -
3120C ASN* 2.9 52.9 + - - +
3122C TYR* 4.2 10.8 - - + -
3138C TRP* 3.9 25.6 - - + -
3149C ALA* 3.6 21.1 + - - +
3152C TYR* 3.8 22.2 + - + +
3154C GLY 5.3 0.4 - - - +
3165C VAL* 4.3 9.8 - - + -
3166C VAL* 1.3 74.5 - - - +
3168C ILE* 1.3 61.4 + - - +
3476C PHE* 4.9 2.5 - - + -
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Residues in contact with ILE3168 (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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3055C PHE* 4.8 0.4 - - + -
3118C TYR 4.0 3.4 - - - -
3119C LEU* 4.0 7.6 - - + -
3137C VAL* 3.6 25.4 - - + -
3138C TRP* 3.3 16.1 + - - +
3139C ILE* 4.0 24.9 - - + -
3140C HIS* 3.7 14.4 + - - +
3149C ALA* 3.5 9.5 - - - +
3166C VAL* 4.0 12.1 - - + -
3167C THR* 1.3 77.9 - - - +
3169C GLN* 1.3 69.8 + - - +
3170C TYR* 4.5 3.6 - - + -
3194C GLN* 4.1 25.6 - - + +
3197C ALA* 3.9 33.2 - - + -
3198C LEU* 5.6 2.2 - - + -
3201C VAL* 5.7 0.4 - - + -
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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