Contacts of the strand formed by residues 677 - 680 (chain F) in PDB entry 6T8B
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 ASP 677 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418F ARG* 3.9 6.2 + - - +
470F SER 4.5 0.8 + - - -
652F PHE* 2.9 25.2 + - - +
672F LEU* 3.3 11.7 - - - +
673F LEU* 3.2 35.4 + - - +
674F GLY 3.8 5.7 + - - +
676F GLY* 1.3 73.9 - - - +
678F MET* 1.3 60.2 + - - +
690F ARG* 2.5 45.9 + - - -
691F VAL 3.6 6.6 - - - +
692F HIS* 3.3 21.8 + - - +
693F GLY 4.6 0.2 - - - +
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Residues in contact with MET 678 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443F LEU* 4.2 31.9 - - + +
475F GLY* 5.2 6.7 - - - -
479F MET* 5.3 0.7 - - + -
650F ILE* 4.1 25.4 - - + -
651F ALA 3.2 11.9 - - - +
652F PHE* 3.5 39.7 - - + -
676F GLY 3.9 0.8 - - - -
677F ASP* 1.3 76.9 - - - +
679F LEU* 1.3 70.6 + - - +
680F TYR* 4.3 3.6 - - - +
690F ARG* 3.8 3.6 - - - +
691F VAL* 2.9 51.3 + - + +
693F GLY* 3.7 23.8 - - - -
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Residues in contact with LEU 679 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398F ARG* 3.9 25.1 - - - +
649F ARG 3.6 9.2 - - - +
650F ILE* 3.6 8.5 - - - -
651F ALA 2.9 11.0 + - - +
664F LEU* 3.8 22.2 - - + +
667F GLY 5.0 2.2 - - - +
668F GLY 3.8 9.0 - - - +
669F ALA* 3.6 37.2 - - + +
672F LEU* 3.6 17.9 - - + -
678F MET* 1.3 73.9 - - - +
680F TYR* 1.3 66.5 + - - +
681F LEU 3.3 2.8 + - - -
688F PRO* 4.0 9.8 - - + +
689F ILE 3.9 2.7 - - - -
690F ARG* 3.6 35.7 - - + +
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Residues in contact with TYR 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443F LEU* 3.5 26.9 - - + -
452F ILE* 4.9 4.7 - - + -
454F THR* 3.4 34.0 - - + +
459F MET* 3.8 16.0 - - - +
462F LEU* 5.1 0.7 - - + -
648F THR* 3.5 30.8 - - + +
650F ILE* 3.6 23.6 - - + -
678F MET* 3.9 5.8 - - - +
679F LEU* 1.3 71.7 - - - +
681F LEU* 1.3 57.4 + - - +
682F PRO* 3.4 29.6 - - + +
683F PRO* 4.0 10.4 - - - +
688F PRO* 3.3 1.5 - - - +
689F ILE* 2.7 52.1 + - + +
691F VAL* 4.1 12.8 - - + -
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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