Contacts of the strand formed by residues 699 - 709 (chain A) in PDB entry 5C58
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 PHE 699 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A TYR* 4.3 25.4 - + - -
696A ALA* 2.8 34.5 + - + +
697A GLY 3.0 2.4 + - - -
698A VAL* 1.3 83.1 - - + +
700A TYR* 1.3 84.4 + - - +
701A ALA* 4.0 12.6 - - + -
771A LEU* 4.1 26.0 - - + -
772A GLY 3.3 22.9 - - - -
773A GLY* 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN* 4.9 2.1 + - - -
693A ASN* 5.7 3.6 - - - +
694A TYR 3.2 13.2 - - - +
695A ASP* 3.4 15.0 - - + +
696A ALA 4.5 0.2 - - - +
699A PHE* 1.3 86.9 - - - +
701A ALA* 1.3 64.0 + - - +
702A ASP* 5.6 2.5 - - + -
770A THR* 3.6 11.7 - - - +
772A GLY* 2.8 61.0 + - - +
773A GLY* 3.6 4.9 + - - -
774A ARG* 3.6 31.4 - - - -
781A ASP* 3.0 31.6 + - - -
782A ALA 4.5 0.3 + - - -
816A TYR* 2.7 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU* 3.8 4.3 - - + +
693A ASN* 3.3 4.6 + - - -
694A TYR* 2.7 49.8 + - + +
699A PHE* 4.0 18.6 - - + -
700A TYR* 1.3 76.3 - - - +
702A ASP* 1.3 61.3 + - - +
703A LEU 4.3 0.2 - - - -
769A VAL* 6.0 1.6 - - + -
770A THR 3.2 9.4 - - - +
771A LEU* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 5.6 0.9 + - - -
130A GLN* 6.3 0.9 - - - -
145A GLN* 4.3 21.2 + - - +
692A LEU 3.4 3.9 - - - +
693A ASN* 2.7 34.6 + - - +
700A TYR* 5.6 2.0 - - + -
701A ALA* 1.3 73.8 - - - +
703A LEU* 1.3 62.9 + - - +
704A THR* 4.3 15.5 - - - +
768A SER* 3.8 2.1 + - - +
769A VAL* 3.2 5.3 + - - +
770A THR* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A TYR* 4.7 14.4 - - + -
691A GLN* 3.2 4.0 - - - -
692A LEU* 2.7 51.2 + - + +
701A ALA 4.3 0.2 - - - -
702A ASP* 1.3 76.8 - - - +
704A THR* 1.3 82.0 + - - +
705A TYR* 4.6 5.6 - - + +
768A SER 3.3 9.9 - - - +
769A VAL* 4.5 17.5 - - + -
788A PHE* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 3.4 26.9 + - - +
146A THR* 4.5 2.8 - - - -
147A THR* 3.6 22.2 - - + +
690A TYR 3.2 6.5 - - - -
691A GLN* 4.2 9.0 - - + -
702A ASP* 4.3 8.1 - - - +
703A LEU* 1.3 86.5 - - - +
705A TYR* 1.3 63.7 + - - +
706A THR* 6.1 0.2 - - - -
767A GLY* 3.1 5.4 - - - -
768A SER* 2.6 55.8 + - - +
788A PHE* 5.0 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.6 2.0 - - - +
689A GLU* 3.4 2.4 - - - -
690A TYR* 2.7 68.3 + + + +
703A LEU* 4.8 5.4 - - + -
704A THR* 1.3 76.1 - - - +
706A THR* 1.3 74.8 + - - +
707A HIS* 3.8 20.1 + - + -
765A ASP* 3.3 25.4 + - + +
766A ARG 3.6 16.6 - - - -
767A GLY* 4.1 3.1 - - - -
788A PHE* 4.0 31.2 - + + -
790A PRO* 4.0 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR 5.1 1.1 - - - +
147A THR* 3.7 12.3 - - + -
148A GLY* 3.4 30.3 - - - +
150A TYR* 2.9 22.0 + - + +
688A LEU 3.3 9.0 - - - -
689A GLU* 4.5 2.5 - - - -
705A TYR* 1.3 80.8 - - - +
707A HIS* 1.3 60.5 + - - +
708A MET* 3.8 16.3 + - - +
765A ASP* 3.4 24.3 - - - +
766A ARG* 3.1 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A GLY* 3.1 6.3 - - - -
688A LEU* 2.9 49.4 + - + +
690A TYR* 5.1 2.2 - - + -
705A TYR* 3.8 20.3 + + + -
706A THR* 1.3 71.7 + - - +
708A MET* 1.3 66.6 + - - +
709A ILE* 3.5 36.6 - - + +
765A ASP* 2.5 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY* 4.6 3.6 - - - -
150A TYR* 3.6 30.7 - - + +
165A ARG* 3.6 39.7 - - + +
647A PHE* 4.0 21.1 - - + -
686A ARG 3.9 4.3 - - - +
706A THR* 3.8 15.1 + - - +
707A HIS* 1.3 78.2 + - - +
709A ILE* 1.3 62.3 + - - +
710A GLY 4.4 0.3 + - - -
762A LEU* 4.4 15.9 - - + -
763A PRO* 3.4 35.7 - - + +
764A GLY 4.8 2.0 - - - +
765A ASP* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 4.8 13.5 - - + -
684A ARG* 5.2 1.2 - - - +
686A ARG* 3.1 48.5 + - + +
687A GLY* 4.2 14.6 - - - -
688A LEU* 4.9 8.7 - - + -
707A HIS* 3.5 31.9 - - + +
708A MET* 1.3 78.7 - - - +
710A GLY* 1.3 69.1 + - - +
762A LEU* 3.4 11.9 - - - +
----------------------------------------------------------
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