Contacts of the helix formed by residues 617 - 626 (chain A) in PDB entry 2R1Z
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 617 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A SER* 2.7 29.0 + - - +
576A GLY* 5.1 7.2 - - - +
615A GLN* 3.1 19.6 - - + +
616A SER* 1.3 80.9 - - - +
618A LEU* 1.3 64.8 + - - +
619A LYS* 3.7 5.4 + - - -
620A CYS* 3.2 13.9 + - - +
621A MET* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A SER 4.1 0.2 + - - -
617A THR* 1.3 71.5 - - - +
619A LYS* 1.3 60.3 + - + +
621A MET* 3.4 9.7 + - + +
622A LEU* 2.9 62.7 + - + +
690A ASN* 3.4 53.4 - - + +
693A LYS* 4.6 17.3 - - + +
694A LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ILE* 3.5 15.2 - - + +
574A GLY 3.0 28.8 + - - +
575A SER* 4.1 17.1 - - - +
576A GLY 5.0 3.6 - - - +
582A GLN* 6.0 2.0 - - - +
598A THR* 3.6 22.0 + - - +
599A GLU* 5.4 0.7 - - - +
600A PHE* 3.7 30.6 - - + +
607A VAL* 4.2 7.6 - - + +
617A THR* 3.2 5.4 + - - +
618A LEU* 1.3 80.0 - - + +
620A CYS* 1.3 58.0 + - - +
622A LEU* 4.8 0.2 - - - -
623A GLY* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A SER* 3.3 26.7 - - - -
607A VAL* 4.4 11.7 - - - -
609A VAL* 3.5 28.0 - - - -
614A VAL* 4.7 4.9 - - + -
615A GLN* 3.2 31.6 - - - +
617A THR* 3.2 8.7 + - - +
619A LYS* 1.3 77.6 - - - +
621A MET* 1.3 58.9 + - - +
623A GLY* 3.1 3.1 + - - -
624A ILE* 2.8 34.1 + - - +
630A ILE* 4.0 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLN 4.3 0.9 - - - +
616A SER 3.2 24.5 - - - +
617A THR 3.0 19.1 + - - +
618A LEU* 3.8 9.2 - - + +
620A CYS* 1.3 74.7 - - - +
622A LEU* 1.3 58.1 + - - +
624A ILE* 3.2 4.7 + - - +
625A LEU* 3.0 32.1 + - - +
686A HIS* 6.2 1.1 - - + -
690A ASN* 6.0 1.6 - - + +
694A LEU* 3.5 27.4 - - + -
764A ILE* 3.9 40.8 - - + -
767A VAL* 3.6 15.9 - - + +
768A MET* 3.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.6 44.2 - - + +
618A LEU* 2.9 45.8 + - + +
619A LYS* 4.0 0.4 - - - +
621A MET* 1.3 72.9 - - - +
623A GLY* 1.3 65.6 + - - +
625A LEU* 3.9 3.1 - - - +
626A ASN* 2.6 32.7 + - - +
693A LYS* 4.1 20.9 - - + +
694A LEU* 4.0 14.4 - - + -
697A ALA* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.5 18.3 - - - -
607A VAL* 4.0 1.3 - - - -
619A LYS 3.0 14.2 + - - -
620A CYS 3.1 4.0 + - - -
622A LEU* 1.3 77.6 - - - +
624A ILE* 1.3 58.8 + - - +
626A ASN 3.2 1.6 + - - -
627A GLY 3.0 4.5 + - - -
628A CYS* 2.9 33.6 + - - +
630A ILE* 3.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A VAL* 3.6 30.5 - - + -
620A CYS 2.8 18.8 + - - +
621A MET* 3.2 6.9 + - - +
623A GLY* 1.3 72.7 - - - +
625A LEU* 1.3 57.4 + - + +
627A GLY* 3.0 7.4 + - - +
628A CYS 5.0 1.1 - - - +
630A ILE* 4.2 9.9 - - + -
656A GLY 4.5 2.9 - - - +
657A PRO* 4.1 20.0 - - + -
660A SER* 2.4 46.0 + - - -
767A VAL* 3.4 25.8 - - + +
768A MET* 3.8 26.7 - - + +
770A PHE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A MET 3.0 16.2 + - - +
622A LEU 4.1 3.6 - - - +
623A GLY 3.4 0.2 - - - -
624A ILE* 1.3 76.2 - - - +
626A ASN* 1.3 58.2 + - - +
627A GLY 3.3 0.7 - - - -
660A SER* 4.6 0.7 - - - -
670A LYS* 4.7 2.4 - - - +
671A LEU* 3.9 40.7 + - + +
672A PHE* 4.3 4.0 - - + -
694A LEU* 3.2 55.6 - - + +
697A ALA* 3.7 26.5 - - + +
698A GLY* 3.9 8.6 - - - +
767A VAL* 3.8 18.4 - - + -
770A PHE* 4.7 5.6 - - + -
801A GOL 3.3 22.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.5 18.7 - - + -
602A SER* 4.3 23.3 + - - +
604A VAL 5.7 0.2 - - - +
622A LEU* 2.6 27.6 + - - +
623A GLY 3.9 2.5 - - - +
625A LEU* 1.3 79.8 + - - +
627A GLY* 1.3 62.0 + - - +
628A CYS* 3.3 14.7 + - - -
664A ARG* 3.2 22.5 + - - -
670A LYS* 5.1 7.5 - - - +
697A ALA* 4.0 23.6 + - - +
801A GOL 3.7 9.5 - - - -
----------------------------------------------------------
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