Contacts of the strand formed by residues 6985 - 6993 (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 PHE6985 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6955C ILE* 4.1 10.8 - - + -
6959C LEU* 3.7 23.3 - - + -
6963C GLY 3.8 4.0 - - - -
6965C VAL* 3.9 17.5 - - + -
6981C LEU 3.2 23.1 - - - -
6982C MET* 3.3 23.5 + - + +
6983C GLY 3.2 1.3 - - - +
6984C HIS* 1.3 81.4 - - - +
6986C ALA* 1.3 55.1 + - - +
6987C TRP 3.1 17.5 - - - +
7006C GLY* 3.2 31.9 - - - -
7007C CYS 3.6 2.0 - - - +
7008C ASN 3.4 4.9 - - - -
7009C TYR* 3.5 39.9 - + + -
7010C LEU* 4.0 3.6 - - - -
7014C ARG* 2.7 35.7 + - - +
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Residues in contact with ALA6986 (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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6985C PHE* 1.3 73.3 - - - +
6987C TRP* 1.3 64.4 + - + +
7007C CYS 3.6 7.4 - - - +
7008C ASN* 2.9 15.2 + - + +
7010C LEU* 3.9 7.5 - - + +
7014C ARG* 3.3 22.1 + - - +
7074C SER* 3.6 45.3 - - - +
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Residues in contact with TRP6987 (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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6808C ALA* 5.1 2.2 - - + -
6811C ASN* 4.4 14.1 + - - +
6814C LYS* 4.1 14.2 - - - +
6851C TYR* 3.3 24.5 - - - -
6855C LEU* 3.8 24.2 - - + -
6985C PHE* 3.1 5.5 - - - +
6986C ALA* 1.3 81.5 - - + +
6988C TRP* 1.3 86.2 + - - +
6989C THR* 3.6 26.2 - - + -
7005C ILE* 5.2 1.8 - - + -
7007C CYS* 2.8 46.1 + - + +
7014C ARG* 4.3 6.1 - - - +
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Residues in contact with TRP6988 (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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6809C MET* 4.5 7.0 - - - -
6814C LYS* 2.7 59.5 + - + +
6979C TYR* 4.4 7.0 - + - -
6982C MET* 3.6 44.9 - - + +
6987C TRP* 1.3 88.9 - + - +
6989C THR* 1.3 90.3 + - - +
6990C ALA* 4.0 4.9 - - + -
7004C LEU* 4.2 15.3 - - + -
7005C ILE 3.0 15.0 - - - +
7006C GLY* 4.4 0.9 - - - -
7014C ARG* 4.3 2.5 - - - -
7015C GLU* 3.5 25.8 + - - -
7017C ILE* 3.7 11.0 - - + +
7022C MET* 3.5 46.4 - - + -
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Residues in contact with THR6989 (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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6808C ALA* 3.6 7.8 - - + +
6809C MET 3.4 29.5 + - - -
6814C LYS* 3.9 5.1 - - - +
6851C TYR* 3.6 32.8 - - + +
6987C TRP* 3.6 17.7 - - + -
6988C TRP* 1.3 93.0 - - - +
6990C ALA* 1.3 68.0 + - - +
6991C PHE* 4.3 1.8 - - + +
7004C LEU* 3.5 2.1 - - - -
7005C ILE* 2.8 40.4 + - + -
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Residues in contact with ALA6990 (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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6808C ALA* 3.5 1.4 - - - -
6809C MET* 2.9 42.4 + - + +
6979C TYR* 5.7 0.2 - - + -
6988C TRP* 4.0 3.5 - - + -
6989C THR* 1.3 76.5 + - - +
6991C PHE* 1.3 60.8 + - - +
7002C ALA* 4.4 3.4 - - + -
7003C PHE 3.5 4.7 - - - -
7004C LEU* 3.9 18.2 - - + -
7026C TYR* 3.7 33.7 - - + -
7029C TRP* 3.9 4.8 - - - -
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Residues in contact with PHE6991 (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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6805C PRO* 3.8 5.6 - - + -
6806C GLY* 3.5 43.3 - - - -
6807C VAL 3.6 14.4 - - - -
6808C ALA* 4.2 0.9 - - - +
6847C GLN 4.0 8.5 - - - -
6848C LEU* 4.0 19.7 - - + -
6851C TYR* 3.4 53.8 - + + -
6989C THR* 4.0 2.0 - - + -
6990C ALA* 1.3 71.9 - - - +
6992C VAL* 1.3 60.2 + - - +
6993C THR* 3.9 26.2 + - + -
7002C ALA* 3.3 3.0 - - - -
7003C PHE* 2.7 41.4 + + + +
7005C ILE* 3.7 20.9 - - + -
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Residues in contact with VAL6992 (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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6806C GLY* 3.1 1.4 - - - -
6807C VAL 2.9 40.5 + - - +
6991C PHE* 1.3 76.9 - - - +
6993C THR* 1.3 73.6 + - - +
6994C ASN* 4.6 0.5 - - - +
6996C ASN 4.9 1.3 - - - +
6997C ALA* 3.8 17.5 - - + +
7001C GLU 3.8 12.8 - - - +
7002C ALA* 4.0 6.5 - - + +
7029C TRP* 3.9 15.7 - - + -
7030C ARG* 3.6 41.3 - - - +
7035C ILE* 3.8 21.1 - - + -
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Residues in contact with THR6993 (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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6805C PRO 3.8 4.9 - - - -
6844C LYS* 3.6 34.0 - - + +
6847C GLN* 3.5 14.1 - - + -
6848C LEU 4.3 1.6 - - - +
6991C PHE* 3.9 19.6 + - + -
6992C VAL* 1.3 78.9 - - - +
6994C ASN* 1.3 64.9 + - - +
6995C VAL* 3.9 5.5 - - - +
6996C ASN* 3.3 25.5 + - - +
6997C ALA* 3.2 15.9 + - - -
7001C GLU* 4.2 3.1 + - - +
7002C ALA* 5.9 0.2 - - - +
7003C PHE* 4.2 16.3 - - + -
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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