Contacts of the helix formed by residues 663 - 676 (chain A) in PDB entry 4NC6
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 PRO 663 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN* 5.1 2.5 - - - +
659A LEU* 4.4 0.2 - - - -
662A MET* 1.4 89.5 - - + +
664A GLU* 1.3 68.6 + - - +
665A GLU* 3.4 1.6 - - + +
666A GLN* 3.0 29.5 + - + +
667A ALA* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A TYR* 2.6 38.1 + - + +
596A ILE* 4.9 1.9 - - - +
629A ASP* 5.2 1.0 - - - +
630A SER* 2.5 45.8 + - - +
633A LYS* 3.6 20.0 + - - +
634A ILE* 3.8 8.7 - - + +
659A LEU* 3.6 14.0 - - - +
662A MET 3.8 0.2 + - - -
663A PRO* 1.3 73.4 - - - +
665A GLU* 1.3 67.3 + - + +
667A ALA* 3.2 2.6 + - - +
668A PHE* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL* 3.4 21.9 - - + +
592A TYR* 3.8 26.7 - - + -
593A ARG* 2.8 52.5 + - - +
663A PRO* 3.4 2.0 - - + +
664A GLU* 1.3 79.8 - - + +
666A GLN* 1.3 75.5 + - - +
668A PHE* 3.5 5.6 + - - +
669A SER* 3.3 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN* 3.0 37.9 - - - +
584A ASN* 6.2 2.4 - - - +
589A VAL* 4.2 13.1 - - - +
662A MET* 3.6 9.2 - - + -
663A PRO* 3.0 35.2 + - + +
665A GLU* 1.3 89.5 + - - +
667A ALA* 1.3 60.0 + - - +
669A SER* 3.2 8.8 + - - -
670A VAL* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ILE* 3.9 8.3 - - + -
655A ALA* 4.7 1.1 - - - +
658A LEU* 3.6 24.7 - - + +
659A LEU* 3.8 22.9 - - + +
662A MET* 3.6 16.9 - - + -
663A PRO 2.9 12.5 + - - +
664A GLU 3.5 7.9 - - - +
666A GLN* 1.3 73.3 - - - +
668A PHE* 1.3 65.5 + - - +
670A VAL 3.4 0.5 + - - -
671A LEU* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LEU* 4.3 19.7 - - + -
591A LYS* 5.8 0.2 - - + -
592A TYR* 3.3 50.0 - + + -
595A LEU* 3.8 23.1 - - + -
634A ILE* 4.0 22.9 - - + +
637A ALA* 3.8 4.5 - - + -
638A TYR* 3.8 28.5 - - + -
641A TYR* 4.2 8.1 - + + -
664A GLU 3.0 9.9 + - - +
665A GLU 3.6 9.2 - - - +
666A GLN 3.3 0.2 - - - -
667A ALA* 1.3 76.1 - - - +
669A SER* 1.3 65.4 + - - +
671A LEU* 3.2 7.8 + - + +
672A VAL* 2.9 49.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
577A GLN* 6.1 0.7 - - - -
582A CYS* 4.6 9.9 - - - -
585A ASN* 4.6 4.4 + - - +
588A LEU* 3.9 35.1 - - - +
589A VAL* 4.0 12.3 + - - +
665A GLU 3.3 12.0 + - - -
666A GLN* 3.2 13.4 + - - +
668A PHE* 1.3 78.1 - - - +
670A VAL* 1.3 63.8 + - - +
672A VAL* 3.3 4.2 + - - +
673A LYS* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TRP* 4.9 0.7 - - + +
577A GLN* 3.9 15.0 - - + -
580A ALA* 4.6 8.5 - - + -
582A CYS* 3.8 21.8 - - - -
658A LEU* 3.7 25.6 - - + -
662A MET* 3.7 19.3 - - + -
666A GLN 2.9 19.3 + - - +
667A ALA 4.0 3.4 - - - +
669A SER* 1.3 73.6 - - - +
671A LEU* 1.3 60.6 + - - +
673A LYS* 3.1 6.6 + - - +
674A ILE* 2.9 39.4 + - + +
749A LEU* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ILE* 3.7 26.9 - - + +
635A CYS* 5.6 1.8 - - - -
638A TYR* 4.2 18.2 - - + -
651A GLN* 3.8 32.3 - - + +
654A LEU* 3.7 34.8 - - + -
655A ALA* 4.4 16.2 - - + +
658A LEU* 3.7 8.8 - - + +
667A ALA 2.9 19.0 + - - +
668A PHE* 3.2 6.5 + - + +
670A VAL* 1.3 76.9 - - - +
672A VAL* 1.3 63.8 + - - +
674A ILE* 3.2 5.8 + - - +
675A MET* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LEU* 4.2 15.5 - - + -
638A TYR* 4.2 14.1 - - + -
641A TYR* 3.7 39.5 - - + +
668A PHE* 2.9 49.9 + - + +
669A SER 3.6 7.9 - - - +
671A LEU* 1.3 75.7 - - - +
673A LYS* 1.3 54.8 + - + +
675A MET 3.2 0.9 + - - -
676A PHE* 2.8 43.5 + - + +
677A ASP* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ALA* 3.7 23.8 - - + +
581A GLY 4.4 3.4 - - - -
582A CYS* 3.1 48.2 - - - +
585A ASN* 2.9 30.7 - - - +
588A LEU* 3.3 18.9 - - + +
669A SER* 3.0 9.5 + - - +
670A VAL* 3.1 7.4 + - - +
672A VAL* 1.3 76.0 - - + +
674A ILE* 1.3 58.6 + - + +
677A ASP* 2.8 50.4 + - + +
678A TYR* 2.9 15.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LEU* 3.9 34.8 - - + -
658A LEU* 4.5 10.1 - - + -
670A VAL* 2.9 30.2 + - + +
671A LEU* 3.7 4.0 - - - +
673A LYS* 1.3 76.9 - - + +
675A MET* 1.3 64.9 + - - +
678A TYR* 3.4 13.9 - - + +
679A GLY 3.2 9.0 + - - -
680A LEU* 3.2 22.7 + - + -
731A LEU* 3.9 25.8 - - + -
745A ILE* 5.3 4.0 - - + -
748A LEU* 4.9 4.0 - - + -
749A LEU* 3.7 32.8 - - + -
753A ILE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.3 26.7 - - + +
648A CYS* 4.0 20.4 - - + -
651A GLN* 3.6 37.2 - - + +
654A LEU* 4.8 1.8 - - - -
671A LEU* 3.0 27.5 + - + +
672A VAL 3.8 2.7 - - - +
674A ILE* 1.3 78.1 - - - +
676A PHE* 1.3 59.3 + - + +
679A GLY* 3.5 1.6 - - - -
680A LEU* 3.2 35.1 + - + -
681A ARG* 3.0 58.2 + - + +
684A PHE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.4 22.4 - + - -
641A TYR* 3.7 31.0 - + - -
642A ASP* 3.7 16.4 - - + -
672A VAL* 2.8 34.8 + - + +
675A MET* 1.3 75.0 - - + +
677A ASP* 1.3 73.6 + - - +
678A TYR 3.5 0.2 - - - -
679A GLY* 3.5 9.7 + - - -
681A ARG* 3.3 38.5 - - - +
----------------------------------------------------------
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