Contacts of the helix formed by residues 961 - 975 (chain A) in PDB entry 6CIM
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 ASN 961 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A SER* 4.8 7.8 + - - -
600A ASP* 4.5 12.5 - - - +
602A MET* 5.8 1.9 - - - +
621A ARG* 3.0 41.9 + - - +
647A ASN 5.3 4.0 + - - -
648A SER 5.5 0.6 + - - -
649A GLU* 5.5 6.8 - - - +
652A CYS* 4.0 19.4 - - - +
706A GLY* 6.1 0.3 - - - -
958A SER 4.8 4.8 + - - +
959A GLU 3.7 0.6 - - - -
960A GLY* 1.3 73.6 - - - +
962A GLN* 1.3 60.9 + - - +
963A SER* 3.0 2.0 - - - +
964A GLY* 2.9 20.0 + - - +
965A ASN 4.2 2.4 + - - -
31F T 5.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A SER 4.3 12.0 + - - +
959A GLU* 3.3 22.8 + - - +
960A GLY 2.7 4.0 + - - +
961A ASN* 1.3 71.5 - - - +
963A SER* 1.3 59.7 + - - +
964A GLY 3.6 0.2 + - - -
965A ASN* 4.4 4.3 + - - +
966A LYS* 4.6 11.8 - - - +
30F G 4.7 11.1 + - - +
31F T 3.7 45.7 + - - +
32F A 3.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A GLU* 3.4 41.2 + - - +
960A GLY 2.9 12.4 + - - -
961A ASN* 4.9 0.3 - - - -
962A GLN* 1.3 77.2 - - - +
964A GLY* 1.3 68.3 + - - +
966A LYS* 3.0 24.5 + - - +
967A LEU* 3.1 13.8 + - - +
20L A 5.2 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A MET* 4.0 17.9 - - - +
621A ARG* 5.7 2.5 - - - -
649A GLU* 5.8 1.6 - - - -
961A ASN* 2.9 18.1 + - - +
963A SER* 1.3 81.1 + - - +
965A ASN* 1.3 51.0 + - - -
967A LEU* 3.0 13.5 + - - +
968A PHE* 2.7 35.0 + - - +
991A HIS* 5.0 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A MET* 3.5 26.9 - - + +
604A ASP 3.1 21.4 + - - +
605A VAL* 3.9 7.4 - - - +
961A ASN 4.2 3.8 + - - -
962A GLN 4.8 3.8 - - - +
963A SER 3.2 0.8 + - - -
964A GLY* 1.3 71.3 - - - +
966A LYS* 1.3 64.6 + - - +
968A PHE* 3.0 9.6 + - - +
969A ARG* 2.7 40.2 + - - +
30F G 3.2 43.7 + - - +
31F T 3.8 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A GLN 4.6 11.0 - - - +
963A SER* 3.0 13.3 + - - +
965A ASN* 1.3 77.2 - - - +
967A LEU* 1.3 65.1 + - - +
969A ARG* 3.0 10.8 + - - +
970A ARG* 2.8 23.8 + - - +
28F G 4.9 9.0 - - - +
29F T 4.4 21.6 + - - -
30F G 4.4 28.6 + - - -
19L C 5.9 1.3 - - - -
20L A 4.0 27.0 + - - -
21L G 3.6 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 4.4 9.6 - - + -
649A GLU* 3.8 26.5 - - + +
963A SER* 3.1 10.5 + - - +
964A GLY* 3.0 11.6 + - - +
966A LYS* 1.3 77.2 - - - +
968A PHE* 1.3 65.8 - - - +
970A ARG* 3.1 7.8 + - - +
971A PHE* 3.0 57.8 + - + -
991A HIS* 4.1 19.5 - - + +
994A TYR* 3.7 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A MET* 4.2 24.2 - - + -
605A VAL* 3.4 38.1 - - + -
619A ALA* 4.8 3.8 - - + -
657A LEU* 3.8 23.8 - - + -
659A LEU* 4.4 10.8 - - + -
964A GLY 2.7 15.1 + - - +
965A ASN* 3.3 10.3 - - - +
967A LEU* 1.3 73.0 - - - +
969A ARG* 1.3 65.2 + - - +
971A PHE* 3.0 8.2 + - - +
972A ARG* 3.0 34.7 + - + +
984A MET* 3.8 33.2 - - + -
987A VAL* 3.6 26.5 - - + +
991A HIS* 5.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ASP* 4.7 7.3 + - - +
605A VAL* 4.3 21.1 + - + +
606A SER 3.6 18.2 + - - -
607A GLU* 3.7 23.8 + - - +
965A ASN* 2.7 42.2 + - - +
966A LYS* 3.6 8.9 - - - +
968A PHE* 1.3 72.9 - - - +
970A ARG* 1.3 67.2 + - - +
972A ARG* 2.9 18.7 + - - +
973A LYS* 3.0 17.9 + - + +
608C LYS 4.7 11.9 + - - -
29F T 3.6 3.4 + - - -
30F G 2.4 50.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 970 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR 5.4 0.2 + - - -
475A PHE* 3.5 43.5 - - + +
966A LYS 2.8 12.2 + - - +
967A LEU* 3.4 11.4 - - - +
969A ARG* 1.3 74.9 - - - +
971A PHE* 1.3 65.1 + - - +
973A LYS* 2.9 19.2 + - - +
974A MET* 3.1 46.4 + - + +
975A ASN* 5.3 0.4 - - - -
480C GLN* 3.4 28.9 - - - +
974C MET* 6.3 1.4 - - - +
21L G 3.4 29.5 + - - -
22L T 4.3 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A VAL* 4.9 7.2 - - + -
475A PHE* 3.7 24.7 - + - -
967A LEU* 3.0 48.2 + - + -
968A PHE 3.0 6.9 + - - +
970A ARG* 1.3 76.2 - - - +
972A ARG* 1.3 60.8 + - - +
975A ASN* 3.2 37.5 + - + +
976A ALA* 3.4 10.0 + - - +
987A VAL* 4.1 23.2 - - + +
990A HIS* 3.8 35.0 - + + -
991A HIS* 4.0 33.7 - + + -
994A TYR* 3.9 14.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL* 3.4 34.4 + - - +
606A SER* 4.7 1.8 - - - +
607A GLU* 4.9 11.2 - - + +
617A GLU* 3.1 35.2 + - - +
659A LEU* 3.7 14.1 - - - +
968A PHE* 3.0 27.6 + - + +
969A ARG* 2.9 11.3 + - - +
971A PHE* 1.3 77.9 - - - +
973A LYS* 1.3 61.7 + - + +
976A ALA* 3.6 13.9 - - + +
978A GLN* 4.2 15.6 + - - +
980A LYS* 4.4 4.2 - - - +
983A GLU* 3.1 42.0 + - + +
984A MET* 6.1 1.2 - - - -
987A VAL* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 973 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A GLU* 3.4 43.5 + - + +
969A ARG* 3.0 17.8 + - + +
970A ARG* 2.9 8.5 + - - +
972A ARG* 1.3 81.5 - - + +
974A MET* 1.3 70.6 + - + +
975A ASN 3.7 0.6 + - - -
976A ALA 4.9 3.0 + - - +
978A GLN* 4.7 7.9 - - - +
973C LYS* 3.3 35.0 - - - +
22J T 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 974 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 3.4 38.1 - - + +
477A SER* 3.6 23.7 + - - -
970A ARG* 3.1 40.5 + - + +
973A LYS* 1.3 90.4 - - + +
975A ASN* 1.3 71.3 + - - +
976A ALA 3.8 0.7 - - - -
974C MET* 3.9 36.3 - - + +
22J T 3.9 9.6 + - - +
23J G 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 3.9 1.4 + - - +
475A PHE* 3.6 28.9 + - - +
476A LEU 3.2 22.2 - - - +
971A PHE* 3.2 27.9 + - + +
974A MET* 1.3 90.7 + - - +
976A ALA* 1.3 61.5 + - - +
986A ASP* 3.8 1.7 - - - +
990A HIS* 3.1 49.6 + - + +
22J T 3.4 7.0 - - - -
23J G 3.0 23.1 + - - +
----------------------------------------------------------
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