Contacts of the helix formed by residues 613 - 623 (chain A) in PDB entry 1CEZ
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 613 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ASP* 3.6 19.7 + - - +
589A GLY* 3.4 7.8 - - - -
590A THR* 3.0 33.9 + - - +
612A GLY* 1.3 72.9 - - - -
614A LYS* 1.3 52.9 + - - +
615A ALA 3.3 0.2 - - - -
616A LEU* 3.7 9.4 - - + +
617A ALA* 2.7 37.0 + - - +
676A TYR* 3.7 22.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ASP 3.3 13.8 - - - +
586A ALA* 3.8 20.4 - - - +
587A ILE 3.8 11.8 + - - -
588A ASN* 3.5 19.3 - - - +
589A GLY 4.2 1.3 - - - +
590A THR 3.1 17.0 + - - +
591A ASP* 4.1 19.4 + - - +
592A ASN* 5.7 0.2 - - - +
612A GLY 3.1 0.8 - - - -
613A THR* 1.3 81.0 + - - +
615A ALA* 1.3 59.1 + - - +
617A ALA* 3.9 2.1 - - - +
618A GLY* 3.2 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ASN* 3.1 36.5 + - - +
611A LEU* 4.1 13.9 - - + -
612A GLY 3.3 5.3 + - - +
614A LYS* 1.3 77.6 - - - +
616A LEU* 1.3 62.0 + - - +
618A GLY* 3.3 1.9 + - - -
619A GLN* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LYS 4.4 0.7 - - - +
611A LEU* 2.8 59.0 - - + +
612A GLY 2.8 18.2 + - - +
613A THR* 3.7 9.4 - - + +
615A ALA* 1.3 75.3 - - - +
617A ALA* 1.3 64.0 + - - +
619A GLN* 3.4 14.2 + - - +
620A TRP* 3.2 29.8 + - - -
672A GLN* 4.3 6.1 - - + +
673A ALA* 4.1 18.6 - - - +
676A TYR* 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 3.5 29.5 - - + +
585A ASP* 3.5 23.8 - - + -
586A ALA* 3.8 7.2 - - - +
613A THR 2.7 21.9 + - - +
614A LYS 3.9 1.8 - - - +
616A LEU* 1.3 72.2 - - - +
618A GLY* 1.3 64.0 + - - +
620A TRP* 3.3 3.8 + - - +
621A LEU* 3.0 29.6 + - - +
676A TYR* 3.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ALA* 5.1 3.1 - - - +
614A LYS 3.2 13.4 + - - -
615A ALA* 3.3 3.8 + - - -
616A LEU 3.3 0.2 - - - -
617A ALA* 1.3 76.7 - - - +
619A GLN* 1.3 65.1 + - - +
621A LEU* 3.3 11.9 + - - +
622A ALA* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 3.7 16.5 - - - +
615A ALA* 2.9 26.0 + - - +
616A LEU* 3.6 21.0 - - - +
617A ALA 3.3 0.2 - - - -
618A GLY* 1.3 74.3 - - - +
620A TRP* 1.3 63.6 + - + +
622A ALA* 3.0 7.8 + - - +
623A TYR* 3.0 17.3 + - - +
666A MET* 2.8 44.3 + - - +
667A PHE* 3.8 23.0 - - + -
668A THR* 3.2 28.3 + - - +
669A GLN 5.1 0.5 + - - -
673A ALA* 3.9 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 3.9 17.3 - - + -
616A LEU* 3.2 20.8 + - - +
617A ALA 3.8 6.3 - - - +
619A GLN* 1.3 79.0 - - - +
621A LEU* 1.3 53.2 + - - +
623A TYR* 3.1 29.6 + + - +
624A GLY* 2.8 32.2 + - - -
625A VAL* 3.6 24.8 - - + +
629A VAL* 4.7 9.2 - - + -
650A VAL* 4.5 9.6 - - + -
654A THR* 4.7 7.2 - - + -
655A ILE* 4.0 25.1 - - + -
667A PHE* 3.8 23.6 - + - -
673A ALA* 3.1 29.2 + - + +
676A TYR* 3.7 17.7 - + - -
677A MET* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ASN* 4.3 11.7 - - - +
582A LEU* 3.8 29.6 - - + +
583A GLN* 3.6 31.0 - - + +
586A ALA* 3.7 30.3 - - + -
617A ALA 3.0 22.1 + - - +
618A GLY* 3.6 7.6 - - - +
620A TRP* 1.3 73.9 - - - +
622A ALA* 1.3 65.6 + - - +
624A GLY* 3.8 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A GLY 2.9 13.0 + - - +
619A GLN* 3.0 10.5 + - - +
621A LEU* 1.3 78.8 - - - +
623A TYR* 1.3 63.7 + - - +
663A LYS* 4.3 5.5 + - - -
666A MET* 4.0 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLN 3.0 12.1 + - - +
620A TRP* 3.1 30.0 + + - +
622A ALA* 1.3 81.6 - - - +
624A GLY* 1.3 58.8 + - - +
625A VAL 4.1 6.3 - - - -
629A VAL* 3.8 25.2 - - + +
632A ARG* 4.5 4.3 + - - -
654A THR* 4.1 22.3 + - + +
658A ALA* 4.0 16.5 - - + +
663A LYS* 3.3 37.9 + - + +
666A MET* 4.0 9.4 - - + +
667A PHE* 4.0 24.5 - + + -
----------------------------------------------------------
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