Contacts of the strand formed by residues 6892 - 6897 (chain C) in PDB entry 6W75
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 LEU6892 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7094A VAL* 4.2 17.9 - - + +
7095A ASN* 3.6 27.8 - - + +
7096A ASN* 3.5 23.1 - - - +
6862C ASN* 3.5 38.8 - - - +
6863C MET 2.7 14.8 + - - +
6864C ARG* 4.5 7.6 - - + -
6865C VAL* 2.8 31.4 + - - +
6890C GLY 3.5 0.2 + - - -
6891C THR* 1.3 72.3 - - - +
6893C LEU* 1.3 57.5 + - - +
6894C VAL* 4.2 1.6 - - + -
6906C ASP* 3.6 3.4 - - + +
6922C TRP* 4.8 3.7 - - + -
7086C VAL* 3.9 28.9 - - + -
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Residues in contact with LEU6893 (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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6865C VAL* 3.4 29.8 - - + +
6867C HIS* 4.4 13.0 - - + -
6880C THR* 3.9 35.2 - - + +
6883C LEU* 4.1 8.5 - - + -
6884C ARG* 3.4 41.1 - - + +
6887C LEU* 4.3 9.9 - - + -
6891C THR 3.5 1.5 + - - +
6892C LEU* 1.3 72.8 - - - +
6894C VAL* 1.3 69.4 + - - +
6905C ALA* 3.4 8.9 - - + +
6906C ASP* 2.8 44.4 + - - +
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Residues in contact with VAL6894 (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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7094A VAL* 3.7 30.7 - - + -
6865C VAL 2.9 7.7 + - - +
6866C ILE* 3.3 10.0 - - + +
6867C HIS* 2.8 25.6 + - - +
6892C LEU* 5.4 1.1 - - + -
6893C LEU* 1.3 80.4 - - - +
6895C ASP* 1.3 71.0 + - - +
6896C SER* 5.9 0.4 - - - -
6905C ALA* 4.3 0.2 - - - -
6906C ASP* 5.4 0.4 - - + -
6907C SER* 3.3 15.5 - - - +
6909C LEU* 4.8 5.8 - - + -
6922C TRP* 3.6 28.9 - - + -
7088C ILE* 4.0 30.1 - - + -
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Residues in contact with ASP6895 (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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6866C ILE* 5.7 0.4 - - - -
6867C HIS* 3.1 15.5 - - + +
6870C ALA* 3.5 8.7 - - + -
6880C THR* 2.8 23.4 + - + +
6893C LEU* 5.6 0.2 - - + -
6894C VAL* 1.3 79.6 - - - +
6896C SER* 1.3 65.2 + - - +
6901C PHE* 3.4 13.6 - - - -
6903C SER* 2.4 26.9 + - - -
6905C ALA* 3.5 6.7 - - + +
6907C SER 3.0 9.0 + - - +
6908C THR* 2.6 29.3 + - - +
6909C LEU 2.9 23.2 + - - -
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Residues in contact with SER6896 (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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6866C ILE* 5.8 2.5 - - - -
6867C HIS 2.9 8.5 + - - -
6868C PHE* 4.2 22.0 - - - -
6869C GLY 3.0 9.6 + - - -
6870C ALA* 2.9 24.3 + - - +
6894C VAL* 5.9 0.4 - - - -
6895C ASP* 1.3 80.7 + - - +
6897C ASP* 1.3 62.8 + - - +
6901C PHE* 4.1 5.4 - - - -
6909C LEU* 2.9 24.3 + - - +
6911C GLY 4.3 6.4 + - - -
6913C CYS* 5.1 2.4 - - - +
6916C VAL* 3.9 19.4 - - - +
7105C SAM 5.5 1.1 - - - -
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Residues in contact with ASP6897 (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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6869C GLY 3.5 5.9 - - - -
6871C GLY* 2.9 21.7 + - - +
6896C SER* 1.3 77.6 + - - +
6898C LEU* 1.3 65.4 + - - +
6899C ASN* 2.9 18.7 + - - +
6901C PHE* 3.4 21.4 - - + -
6909C LEU 3.2 3.2 + - - -
6910C ILE* 3.3 7.3 - - - +
6911C GLY 2.7 32.6 + - - -
7105C SAM 2.6 61.5 + - - -
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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