Contacts of the helix formed by residues 660 - 675 (chain A) in PDB entry 3ZFM
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 660 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A LEU* 5.5 6.1 - - - +
661A GLU* 1.3 62.7 + - - +
662A LYS* 4.9 5.4 - - + -
663A GLN* 3.4 26.2 - - + +
664A ARG* 3.4 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A THR* 1.3 69.1 - - - +
662A LYS* 1.4 64.3 + - - +
664A ARG* 3.5 7.6 + - - +
665A ARG* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A THR* 5.3 5.6 - - + -
661A GLU* 1.4 79.4 - - - +
663A GLN* 1.4 61.3 + - + +
665A ARG* 3.6 7.8 + - - +
666A ASP* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A PHE* 3.8 24.5 - - + -
655A LEU* 4.0 7.9 - - + +
660A THR* 3.4 27.2 + - + +
661A GLU 3.4 0.6 - - - -
662A LYS* 1.4 79.7 - - + +
664A ARG* 1.4 59.8 + - - +
665A ARG 3.3 0.2 - - - -
666A ASP* 3.5 7.1 + - - -
667A PHE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A LEU* 4.2 12.5 - - + +
660A THR 3.4 18.4 + - - +
661A GLU* 3.7 7.4 - - - +
662A LYS 3.4 0.4 - - - -
663A GLN* 1.4 76.0 - - - +
665A ARG* 1.4 62.1 + - - +
667A PHE* 3.9 0.6 - - - +
668A LEU* 3.3 52.1 + - + +
690A THR* 3.5 27.9 + - - +
695A VAL* 3.5 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A GLU 3.2 14.1 + - - +
662A LYS* 3.6 12.8 - - - +
663A GLN 3.3 0.2 - - - -
664A ARG* 1.4 78.1 - - - +
666A ASP* 1.4 57.5 + - - +
668A LEU* 4.5 3.2 - - - +
669A SER* 3.2 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A PHE* 3.7 27.8 - - + -
662A LYS* 3.0 23.8 + - - +
663A GLN* 3.5 5.0 + - - +
664A ARG 3.3 0.2 - - - -
665A ARG* 1.4 77.7 - - - +
667A PHE* 1.3 63.0 + - - +
669A SER* 2.7 22.3 + - - -
670A GLU* 3.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A PHE* 3.8 33.6 - + + -
633A GLY 5.0 1.1 - - - -
653A LYS* 3.7 19.3 - - + -
654A THR 3.6 31.4 - - - -
655A LEU* 3.8 11.9 - - + -
663A GLN 3.0 18.0 + - - +
664A ARG 3.9 3.6 - - - +
666A ASP* 1.3 78.6 - - - +
668A LEU* 1.3 69.0 + - + +
669A SER 3.5 0.2 + - - -
670A GLU* 3.6 11.3 + - - +
695A VAL* 3.8 39.7 - - + -
697A ILE* 3.3 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ARG* 3.3 51.8 + - + +
665A ARG* 4.7 3.8 - - - +
667A PHE* 1.3 87.9 - - + +
669A SER* 1.4 62.8 + - - +
670A GLU 3.3 0.4 - - - -
671A ALA* 3.4 8.4 + - - +
672A SER* 3.3 18.1 + - - -
688A VAL* 4.1 22.6 - - + +
689A VAL 5.3 0.2 - - - +
690A THR* 3.8 29.4 - - + -
695A VAL* 4.7 8.7 - - + -
696A MET 5.3 1.6 - - - +
697A ILE* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ARG 3.2 18.0 + - - -
666A ASP* 2.7 27.5 + - - -
668A LEU* 1.4 73.8 - - - +
670A GLU* 1.4 64.1 + - - +
672A SER* 3.2 18.0 + - - -
673A ILE* 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ASP 4.5 4.0 - - - +
667A PHE* 3.6 12.2 + - - +
668A LEU 3.3 0.4 - - - -
669A SER* 1.4 79.5 + - - +
671A ALA* 1.4 55.0 + - - +
673A ILE* 3.4 11.1 + - - +
674A MET* 3.0 44.0 + - - +
697A ILE* 4.1 20.1 - - - +
699A THR* 6.1 0.2 - - - +
763A SER* 4.9 2.6 + - - -
764A ASP* 3.9 15.7 + - - +
765A PHE* 3.8 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A PHE 4.3 0.4 + - - -
668A LEU 3.4 10.1 + - - +
669A SER 3.3 0.4 - - - -
670A GLU* 1.4 76.2 + - - +
672A SER* 1.3 56.1 + - - +
673A ILE 3.4 0.2 - - - -
674A MET* 3.8 9.4 - - - -
675A GLY* 2.8 25.8 + - - -
685A LEU* 3.3 27.0 - - + +
688A VAL* 3.7 29.4 - - + -
697A ILE* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU 3.3 11.8 + - - -
669A SER* 3.2 16.0 + - - -
671A ALA* 1.3 75.4 - - - +
673A ILE* 1.3 63.5 + - - +
675A GLY* 3.8 3.3 + - - -
676A GLN* 3.4 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A SER* 3.3 23.9 + - - +
670A GLU 3.7 4.5 - - - +
672A SER* 1.3 77.1 - - - +
674A MET* 1.4 61.7 + - - +
676A GLN* 3.2 28.3 + - - +
677A PHE* 3.3 21.9 - - + -
742A TYR* 3.8 26.5 - - + +
765A PHE* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU* 3.0 34.4 + - + +
671A ALA* 3.8 8.3 - - - +
673A ILE* 1.4 78.3 - - - +
675A GLY* 1.3 55.2 - - - +
676A GLN 3.2 0.4 - - - -
677A PHE* 3.2 33.0 + - - +
682A VAL* 5.8 0.2 - - + -
683A ILE* 3.3 39.1 - - + +
685A LEU* 3.6 29.5 + - + +
697A ILE* 5.4 0.9 - - - -
699A THR* 3.6 31.9 - - + -
763A SER* 5.7 2.9 - - - -
765A PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA 2.8 19.0 + - - -
672A SER 4.2 2.2 - - - -
673A ILE 3.3 0.4 - - - -
674A MET* 1.3 76.2 - - - +
676A GLN* 1.3 59.4 + - - +
677A PHE 3.3 5.6 + - - +
685A LEU* 4.0 15.9 - - - -
----------------------------------------------------------
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