Contacts of the strand formed by residues 680 - 687 (chain G) in PDB entry 6C3P
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 GLN 680 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677G CYS 4.4 8.6 + - - +
678G CYS 3.4 11.7 - - - +
679G VAL* 1.3 77.7 - - - +
681G ILE* 1.3 74.6 + - - +
682G MET* 4.6 16.5 - - + +
701G ILE* 2.9 23.3 - - - +
702G ARG* 2.5 45.0 + - - +
736G ALA 3.6 0.3 - - - +
737G VAL* 3.4 1.7 - - - +
738G PHE* 3.3 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 681 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G VAL* 5.0 2.9 - - + -
680G GLN* 1.3 87.1 - - - +
682G MET* 1.3 68.6 + - - +
683G GLY 3.9 0.2 - - - -
684G GLY* 3.5 32.8 - - - +
686G PHE* 4.5 6.1 - - + -
699G ILE* 3.6 15.7 - - + -
700G THR* 3.2 11.3 - - - +
701G ILE* 3.0 49.3 + - + +
722G LEU* 5.0 4.5 - - + -
726G ALA* 4.9 15.9 - - + -
735G GLY* 4.6 0.2 - - - -
736G ALA 3.2 12.1 - - - +
737G VAL* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 682 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680G GLN* 4.6 20.4 - - - +
681G ILE* 1.3 75.0 - - - +
683G GLY* 1.3 67.0 + - - +
684G GLY 3.5 0.4 - - - -
700G THR* 4.5 5.8 - - + -
702G ARG* 5.8 4.5 - - - +
735G GLY* 3.5 14.9 - - - -
736G ALA* 3.2 17.0 + - + +
738G PHE* 4.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 683 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682G MET* 1.3 74.1 - - - +
684G GLY* 1.3 65.3 + - - +
685G TYR* 3.1 22.6 + - - -
698G ASN* 3.8 23.3 - - - -
699G ILE 3.2 10.2 + - - -
700G THR* 3.5 8.0 + - - -
734G SER* 4.6 0.3 + - - -
735G GLY* 3.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 684 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681G ILE* 3.5 19.1 - - - -
682G MET 3.5 0.8 - - - -
683G GLY* 1.3 72.3 - - - +
685G TYR* 1.3 57.1 + - - -
686G PHE* 3.8 3.6 - - - -
697G SER* 3.3 3.6 + - - -
698G ASN 2.6 26.9 + - - -
699G ILE* 2.5 40.0 + - - +
734G SER 3.7 4.9 - - - -
735G GLY* 4.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 685 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683G GLY* 3.1 28.7 - - - -
684G GLY* 1.3 71.2 - - - -
686G PHE* 1.3 62.5 + - - +
694G PRO* 5.3 5.2 - - + -
696G LEU 3.1 4.7 - - - +
697G SER* 3.4 26.7 - - - -
698G ASN* 3.4 29.4 + - + +
732G LYS* 3.0 8.0 - - - +
733G VAL* 2.8 28.0 + - + -
734G SER* 2.6 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 686 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681G ILE* 4.6 5.8 - - + -
684G GLY* 3.8 11.0 - - - -
685G TYR* 1.3 74.9 - - - +
687G THR* 1.3 55.4 + - - +
694G PRO* 3.1 4.6 - - - +
695G THR 2.5 29.7 + - - -
696G LEU* 2.7 44.7 + - + +
699G ILE* 3.5 27.1 - - + -
722G LEU* 4.5 3.1 - - + -
725G ALA* 3.4 32.1 - - + -
726G ALA 5.3 0.4 - - - -
730G MET* 3.3 22.9 - - - -
731G GLN 3.5 3.6 - - - -
732G LYS* 3.4 34.1 - - + +
733G VAL* 4.5 2.2 - - - +
734G SER 4.9 0.9 - - - -
735G GLY* 6.0 0.4 - - - -
737G VAL* 4.3 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 687 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686G PHE* 1.3 77.6 - - - +
688G TRP* 1.3 60.8 + - - +
689G THR 3.1 28.8 + - - +
690G PRO* 4.1 8.5 - - + +
692G GLY 4.4 0.6 + - - +
693G ILE 2.8 22.5 + - - -
694G PRO* 3.6 10.3 - - - +
695G THR* 3.4 7.2 - - - -
730G MET* 3.0 14.4 - - - +
731G GLN* 2.6 42.3 + - + +
733G VAL* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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