Contacts of the helix formed by residues 609 - 619 (chain A) in PDB entry 4EGA
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 THR 609 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A GLY 3.3 11.7 + - - -
605A GLU* 3.1 18.4 + - - +
608A ASP* 1.3 79.6 - - - +
610A LEU* 1.3 64.9 + - - +
613A LEU* 3.3 15.3 + - - +
669A PHE* 4.1 11.8 - - + -
672A LEU* 3.6 31.6 - - + -
673A ARG* 4.1 18.0 + - + +
676A ASN* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLU 3.1 7.5 + - - +
606A LEU* 3.6 8.1 - - + +
609A THR* 1.3 77.2 - - - +
611A GLY* 1.3 68.1 + - - +
613A LEU* 3.1 15.4 + - + +
614A VAL* 3.1 30.1 + - + +
669A PHE* 4.4 6.5 - - + -
672A LEU* 4.0 31.6 - - + -
706A VAL* 5.0 3.4 - - + -
709A THR* 5.1 0.9 - - - +
710A THR* 4.3 8.5 - - - +
713A LEU* 4.1 21.8 - - + -
717A LEU* 4.3 13.0 - - + -
724A ILE* 4.1 24.5 - - + -
761A LEU* 5.2 0.2 - - + -
762A PHE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU 2.8 20.0 + - - -
607A ALA* 3.3 8.0 + - - -
610A LEU* 1.3 72.4 - - - +
612A ASN* 1.3 63.4 + - - +
614A VAL* 3.2 12.0 + - - +
615A MET* 3.2 21.7 + - - +
761A LEU* 4.4 14.8 - - - +
762A PHE* 4.3 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ALA 2.7 11.1 + - - +
608A ASP* 3.0 29.3 - - - +
609A THR 4.3 0.4 - - - +
610A LEU 3.3 0.2 - - - -
611A GLY* 1.3 73.5 - - - +
613A LEU* 1.3 64.0 + - - +
615A MET* 3.3 5.8 + - - +
616A ARG* 3.0 51.3 + - - +
676A ASN* 3.2 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A THR 3.3 11.3 + - - +
610A LEU* 3.1 6.8 + - + +
612A ASN* 1.3 80.1 - - - +
614A VAL* 1.3 62.5 + - - +
616A ARG* 3.5 10.8 + - - +
617A CYS* 3.2 27.0 + - - +
672A LEU* 3.8 21.3 - - + +
675A ILE* 3.4 35.7 - - + -
676A ASN* 3.3 41.3 - - - +
679A VAL* 4.5 11.0 - - + -
702A THR* 4.6 3.9 - - + +
706A VAL* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 3.1 23.3 + - + +
611A GLY 3.2 6.9 + - - +
613A LEU* 1.3 77.1 - - - +
615A MET* 1.3 61.6 + - + +
617A CYS* 3.6 6.9 - - - -
618A THR* 2.8 30.8 + - + +
706A VAL* 3.7 22.7 - - + -
724A ILE* 4.1 15.0 - - + -
727A MET* 3.9 29.4 - - + -
728A LEU* 4.4 15.7 - - + -
761A LEU* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A GLY* 3.2 16.6 + - - +
612A ASN* 3.9 7.0 - - - +
614A VAL* 1.3 76.7 - - + +
616A ARG* 1.3 65.2 + - - +
618A THR* 3.4 6.0 + - - +
619A SER* 2.8 29.0 + - - -
727A MET* 4.7 21.3 - - - +
759A GLU* 4.3 20.0 - - + +
760A VAL* 5.1 8.1 - - + -
761A LEU* 4.8 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ASN* 3.0 40.8 + - - +
613A LEU* 3.7 10.1 - - + +
615A MET* 1.3 77.7 - - - +
617A CYS* 1.3 60.9 + - - +
618A THR 3.3 0.3 + - - -
619A SER* 3.4 8.9 + - - -
622A ILE* 3.3 39.8 - - + +
676A ASN* 3.2 34.8 + - - +
679A VAL* 3.8 32.2 - - + +
680A THR* 4.1 13.5 + - - -
685A TRP* 4.0 22.2 - - + -
702A THR* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU 3.2 16.3 + - - +
614A VAL* 3.6 14.6 - - - -
616A ARG* 1.3 76.9 - - - +
618A THR* 1.3 58.8 + - - +
622A ILE* 5.3 0.2 - - - -
623A ASN* 3.3 22.4 + - - +
699A LEU* 3.6 17.6 - - + +
702A THR* 3.4 30.3 - - + -
703A LEU* 3.4 34.6 - - + +
706A VAL* 4.4 8.7 - - - -
728A LEU* 4.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A VAL* 2.8 27.2 + - + +
615A MET* 3.4 13.0 + - - +
616A ARG 3.2 0.2 - - - -
617A CYS* 1.3 83.2 - - - +
619A SER* 1.3 63.1 + - - +
620A ALA 3.5 1.6 + - - -
623A ASN* 4.4 3.4 - - - +
626A GLY* 5.9 0.3 - - - -
703A LEU* 4.6 0.2 - - + -
727A MET* 4.3 17.3 - - + +
728A LEU* 3.9 25.8 - - + -
752A LEU* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A MET 2.8 18.1 + - - -
616A ARG* 3.4 11.2 + - - -
617A CYS 3.7 0.2 - - - -
618A THR* 1.3 76.1 - - - +
620A ALA* 1.3 58.3 + - - +
621A LYS* 3.4 18.9 + - - +
622A ILE* 3.0 11.5 + - - -
623A ASN* 2.6 36.0 + - - -
----------------------------------------------------------
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