Contacts of the strand formed by residues 710 - 718 (chain A) in PDB entry 1L5G
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 SER 710 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A MET* 4.3 8.9 + - - +
708A ASP* 3.4 9.6 + - - +
709A THR* 1.3 94.0 - - - +
711A VAL* 1.3 64.0 + - - +
712A LYS* 5.3 2.4 - - - +
733A LYS* 3.3 26.8 + - - +
734A VAL 3.0 25.4 - - - -
735A ASP* 3.8 5.4 - - - -
736A LEU* 3.6 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ILE* 3.8 26.5 - - + -
648A PRO* 4.7 7.0 - - + -
650A GLN* 2.9 39.3 - - + +
701A VAL* 4.5 13.5 - - + -
703A GLN* 5.8 0.2 - - - -
704A GLN* 5.7 0.9 - - + +
707A MET* 5.5 1.8 - - + +
710A SER* 1.3 74.4 - - - +
712A LYS* 1.3 62.1 + - - +
713A PHE* 5.0 12.8 - - + -
733A LYS* 3.4 2.1 - - - +
734A VAL* 2.9 34.3 + - + +
736A LEU* 3.4 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A SER 4.3 1.2 - - - +
647A ILE 4.9 0.2 - - - -
648A PRO* 3.5 23.5 - - - +
710A SER 5.3 2.7 - - - +
711A VAL* 1.3 77.5 - - - +
713A PHE* 1.3 66.3 + - - +
714A ASP* 3.7 25.7 + - - +
731A SER* 3.9 14.4 - - - +
732A HIS 3.6 4.7 - - - +
733A LYS* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 3.5 33.4 - - + -
627A LEU* 3.7 26.5 - - + -
645A VAL* 4.1 7.2 - - + -
646A SER 3.3 7.6 - - - +
647A ILE* 3.4 38.6 - - + -
648A PRO* 4.4 5.4 - - + -
651A ALA* 4.0 15.5 - - + -
699A PHE* 3.7 22.7 - + - -
701A VAL* 6.1 1.8 - - + -
711A VAL* 5.0 13.2 - - + -
712A LYS* 1.3 80.0 - - - +
714A ASP* 1.3 62.4 + - - +
715A LEU* 5.1 2.5 - - + -
731A SER* 3.2 6.1 + - - -
732A HIS* 2.6 53.1 + + + +
734A VAL* 5.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ILE 3.4 5.7 - - - +
645A VAL* 3.7 1.7 - - - -
646A SER* 2.9 52.7 + - - +
712A LYS* 3.7 21.3 - - - +
713A PHE* 1.3 73.4 - - - +
715A LEU* 1.3 62.0 + - - +
729A VAL* 4.5 17.1 - - + +
730A VAL 3.6 1.7 - - - -
731A SER* 3.0 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL* 3.4 21.3 - - + +
610A VAL* 3.5 44.4 - - + -
627A LEU* 5.0 6.5 - - + -
629A VAL* 4.2 16.2 - - + -
643A LEU* 4.6 3.8 - - + -
644A ILE 4.0 1.1 - - - -
645A VAL* 3.5 43.7 - - + -
713A PHE* 5.1 2.2 - - + -
714A ASP* 1.3 76.7 - - - +
716A GLN* 1.3 61.2 + - - +
728A PRO 3.6 0.5 - - - +
729A VAL* 3.3 1.0 - - - -
730A VAL* 2.5 53.7 + - + +
732A HIS* 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL* 3.4 11.0 - - - +
643A LEU* 4.2 2.8 - - - +
644A ILE* 3.1 37.3 + - + +
715A LEU* 1.3 78.2 - - - +
717A ILE* 1.3 66.5 + - - +
718A GLN* 3.6 28.2 - - - +
726A VAL* 3.8 15.4 - - - +
727A SER 3.1 27.7 + - - +
728A PRO 3.3 6.7 - - - +
729A VAL* 3.1 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU* 4.0 22.7 - - + -
607A GLU 3.7 36.6 - - - +
608A VAL* 3.4 15.5 - - + -
631A ALA* 3.9 19.1 - - + -
632A GLN 4.1 3.6 - - - +
641A ALA* 4.7 2.2 - - + -
642A GLU 3.6 8.7 - - - +
643A LEU* 4.2 8.1 - - + +
683A LEU* 3.4 29.2 - - + -
687A MET* 5.1 0.2 - - + -
716A GLN* 1.3 74.6 - - - +
718A GLN* 1.3 72.7 + - - +
726A VAL* 3.2 6.6 - - - +
727A SER* 2.4 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU* 4.6 0.4 - - - -
640A GLU 3.5 1.4 - - - +
641A ALA* 3.2 4.5 - - - -
642A GLU* 3.2 52.6 + - + +
644A ILE* 3.6 29.4 - - + +
716A GLN* 3.6 24.2 - - - +
717A ILE* 1.3 76.9 - - - +
719A SER* 1.3 65.3 + - - +
725A LYS* 3.6 7.2 - - + -
726A VAL* 4.0 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