Contacts of the strand formed by residues 694 - 701 (chain A) in PDB entry 5A7R
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 LEU 694 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 3.9 18.8 - - + -
484A ILE* 4.0 16.8 - - + -
489A LEU* 3.9 24.5 - - + -
495A PRO* 3.7 20.0 - - + -
624A THR* 3.9 13.5 - - + -
625A MET 3.3 6.7 - - - +
626A SER* 3.7 18.6 - - - +
627A GLN* 4.8 1.0 - - - +
693A GLY* 1.3 81.1 - - - +
695A VAL* 1.3 69.4 + - - +
785A GLY 3.9 5.9 - - - +
814A TRP* 3.3 25.8 - - + +
815A GLN* 3.0 7.0 + - + -
816A ARG* 3.4 26.1 - - + +
817A ARG 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE 3.7 1.7 - - - +
624A THR* 3.4 2.7 - - - -
625A MET* 2.9 32.2 + - - +
627A GLN* 4.0 15.0 - - + -
630A ILE* 3.7 26.7 - - + -
694A LEU* 1.3 81.7 - - - +
696A THR* 1.3 65.4 + - - +
697A PHE* 3.7 20.9 - - + -
764A GLU* 4.4 6.5 - - + +
783A ILE* 3.8 17.9 - - + -
784A THR 3.4 12.6 - - - +
785A GLY 3.8 13.7 - - - +
786A THR* 3.9 11.4 - - + +
816A ARG* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A HIS* 4.6 2.5 - - + +
622A SER* 4.2 9.9 - - - -
623A ILE 3.3 5.8 - - - +
624A THR* 2.7 25.0 + - - +
695A VAL* 1.3 73.1 - - - +
697A PHE* 1.3 64.2 + - - +
698A THR* 3.6 20.0 - - - +
782A ILE 3.7 0.9 - - - +
783A ILE* 3.3 8.3 - - - +
784A THR* 2.9 36.2 + - - +
814A TRP* 4.4 1.2 - - - -
816A ARG* 3.0 38.9 + - - +
1986A PPI 4.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A LEU* 4.2 8.7 - - + +
621A HIS 3.9 0.9 - - - +
622A SER* 3.2 2.4 - - - -
623A ILE* 2.8 47.5 + - + +
625A MET* 3.9 22.9 - - - -
630A ILE* 4.1 3.1 - - + -
695A VAL* 3.7 29.8 - - + -
696A THR* 1.3 75.9 - - - +
698A THR* 1.3 60.8 + - - +
764A GLU 3.8 15.5 - - - -
765A LEU* 4.7 1.8 - - - -
767A ILE* 3.5 24.0 - - + -
768A SER* 4.0 19.3 - - - -
771A PHE* 3.7 29.8 - + + -
781A LEU* 4.6 4.3 - - + -
782A ILE 3.6 3.4 - - - -
783A ILE* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A HIS 3.5 4.9 - - - +
622A SER* 2.7 25.6 + - - +
696A THR* 3.6 10.7 - - - +
697A PHE* 1.3 73.7 - - - +
699A ARG* 1.4 73.4 + - - +
700A GLN* 3.8 5.9 + - + +
781A LEU* 3.4 7.7 - - - +
782A ILE* 2.8 62.0 + - + +
1986A PPI 4.8 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A LEU* 2.9 41.0 + - + +
616A ALA 3.2 23.4 + - - -
617A ALA* 3.8 6.5 - - - +
619A MET* 3.5 16.8 - - + +
620A ASN* 3.4 6.4 - - - +
621A HIS 3.0 30.3 + - - +
697A PHE 4.3 0.4 - - - -
698A THR* 1.4 77.6 - - - +
700A GLN* 1.3 63.4 + - - +
772A THR* 3.6 10.7 - - - +
773A GLU 3.0 20.8 + - - +
774A VAL 3.0 23.4 + - - -
775A LEU* 3.8 8.7 - - + +
779A GLU* 2.7 42.2 + - - +
780A CYS 3.6 11.2 - - - +
781A LEU* 4.2 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ASN* 3.4 7.2 - - - +
698A THR* 3.8 5.0 + - + +
699A ARG* 1.3 76.0 - - - +
701A SER* 1.3 63.2 + - - +
702A LEU* 3.9 25.6 - - + +
779A GLU* 3.2 6.0 - - - +
780A CYS* 3.0 44.5 + - - +
782A ILE* 4.3 16.1 - - + +
850A CYS* 2.8 34.4 + - - +
853A LEU 3.0 19.9 + - - +
854A ARG* 4.0 6.1 - - - +
855A PRO* 3.7 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.6 16.3 - - - +
619A MET 4.1 8.1 - - - -
620A ASN* 2.9 32.5 + - - +
700A GLN* 1.3 74.9 - - - +
702A LEU* 1.3 64.0 + - - +
703A GLU 4.2 0.7 + - - -
778A ASN* 3.3 21.9 + - - -
779A GLU* 3.5 23.8 + - - +
----------------------------------------------------------
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