Contacts of the strand formed by residues 686 - 691 (chain C) in PDB entry 6CIM
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 GLU 686 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C GLU 3.4 1.2 - - - +
519C TRP* 3.3 9.1 - - - -
520C GLN* 2.9 57.6 + - + +
590C PRO* 6.2 1.8 - - - -
685C SER* 1.3 77.7 + - - +
687C LEU* 1.3 61.0 + - - +
688C THR* 3.9 4.0 + - - +
697C THR* 3.7 26.5 + - + +
698C PHE 3.8 3.6 - - - +
699C LYS* 4.9 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PHE* 3.6 27.4 - - + -
518C GLU 3.4 6.1 - - - +
519C TRP* 3.4 42.6 - - + +
563C LEU* 5.3 0.2 - - + -
564C VAL* 4.1 16.6 - - + +
567C LEU* 4.3 6.5 - - + -
686C GLU* 1.3 72.4 - - - +
688C THR* 1.3 64.6 + - - +
689C LEU* 4.0 7.1 + - + -
696C ARG 3.6 0.9 - - - +
697C THR* 3.2 6.9 - - - -
698C PHE* 2.9 57.7 + - + +
700C PHE* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 688 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PHE* 3.3 9.4 - - - +
518C GLU* 2.8 56.2 + - + +
520C GLN* 5.3 7.3 + - - +
686C GLU* 3.9 4.9 + - - +
687C LEU* 1.3 72.0 - - - +
689C LEU* 1.3 63.2 + - - +
695C PRO* 4.5 17.5 - - + -
696C ARG 3.4 10.1 - - - +
697C THR* 3.8 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 689 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C HIS* 4.7 3.1 - - + -
516C PRO 3.4 23.1 - - - +
517C PHE* 4.1 3.8 - - + -
564C VAL* 3.8 27.8 - - + +
567C LEU* 4.2 17.7 - - + -
568C MET* 3.7 33.0 - - + -
687C LEU* 4.5 8.1 - - + -
688C THR* 1.3 77.0 - - - +
690C GLU* 1.3 66.8 + - - +
691C MET* 3.5 3.9 + - + +
695C PRO* 4.4 1.8 - - - -
696C ARG* 2.8 33.0 + - - +
698C PHE* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 690 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C PRO* 4.8 11.2 + - + +
568C MET* 3.5 23.2 - - - +
689C LEU* 1.3 76.8 - - - +
691C MET* 1.3 61.6 + - - +
692C GLY 4.4 0.2 + - - -
693C GLY* 3.2 41.3 - - - +
694C ILE 3.6 4.9 - - - +
695C PRO* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 691 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C LEU 4.5 6.3 - - - +
568C MET* 3.9 15.7 - - - +
571C GLU* 4.0 26.7 - - + +
574C ILE* 3.9 40.4 - - + -
575C LEU* 3.9 16.8 - - + -
591C PHE* 5.2 2.0 - - + -
689C LEU* 3.5 7.8 + - + +
690C GLU* 1.3 78.0 - - - +
692C GLY* 1.3 67.6 + - - +
693C GLY 3.2 1.6 - - - -
694C ILE 2.9 21.5 + - - +
696C ARG* 3.0 35.2 + - + +
698C PHE* 3.8 25.6 - - + -
----------------------------------------------------------
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