Contacts of the helix formed by residues 996 - 1004 (chain C) 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 SER 996 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C LEU* 4.8 13.0 - - - +
569C ASP* 3.0 23.1 + - - -
653C LYS* 4.1 4.7 - - - +
992C TRP* 3.5 8.2 + - - -
993C LEU* 3.3 11.3 + - - +
994C TYR 3.5 0.6 - - - +
995C THR* 1.3 75.0 - - - +
997C LYS* 1.3 62.8 + - - +
998C TYR* 4.0 1.1 - - - +
999C LEU* 3.1 35.5 + - - +
1000C GLN* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 997 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASP* 2.4 31.6 + - - +
570C MET* 3.6 37.1 - - + +
573C ASP* 4.5 15.7 - - - +
641C PHE* 4.0 11.7 - - - -
643C GLU* 2.8 35.5 + - - -
644C PRO* 5.5 2.7 - - - +
651C CYS* 4.0 14.5 - - - +
653C LYS* 5.5 2.9 - - - +
995C THR 3.5 4.2 + - - +
996C SER* 1.3 67.5 - - - +
998C TYR* 1.3 54.0 + - - +
1000C GLN* 3.6 19.8 + - - +
1001C LYS* 3.0 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 998 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLN* 4.6 5.0 + - - -
465C ALA* 3.8 25.5 - - + +
509C VAL* 6.6 0.2 - - + -
510C LEU* 3.6 25.4 - - + -
569C ASP* 3.3 30.5 + - - +
572C GLU* 4.2 26.7 - - - -
996C SER* 3.1 2.4 - - - +
997C LYS* 1.3 80.1 - - - +
999C LEU* 1.3 69.8 + - + +
1001C LYS* 3.5 18.0 + - + +
1002C PHE* 3.7 32.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 999 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ALA 3.2 29.2 - - - +
468C LEU* 4.3 11.9 - - + +
469C ALA* 3.6 21.6 - - + +
472C VAL* 5.3 2.9 - - + -
473C ASN* 6.0 3.1 - - - +
510C LEU* 3.8 30.1 - - + -
993C LEU* 3.5 28.5 - - + +
996C SER* 3.1 19.5 + - - +
998C TYR* 1.3 82.3 - - + +
1000C GLN* 1.3 66.6 + - + +
1002C PHE* 3.1 10.9 + - + +
1003C MET* 3.0 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1000 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C ASN* 5.5 7.2 - - - +
645C LYS* 5.9 0.2 + - - -
650C LEU* 3.0 54.0 + - + +
994C TYR 3.6 12.1 + - - +
995C THR 3.3 17.4 + - - -
996C SER 3.2 10.1 + - - +
997C LYS* 3.6 25.1 + - - +
998C TYR 3.3 0.4 - - - -
999C LEU* 1.3 75.5 - - + +
1001C LYS* 1.3 65.9 + - + +
1003C MET* 3.1 10.8 + - - +
1004C ASN* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1001 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C GLU* 5.1 12.8 - - - +
573C ASP* 2.6 41.6 + - - -
997C LYS* 3.0 35.1 + - - +
998C TYR* 3.6 11.7 - - + +
999C LEU 3.2 0.2 - - - -
1000C GLN* 1.3 75.0 - - + +
1002C PHE* 1.3 69.1 + - + +
1004C ASN* 3.0 17.3 + - - +
1005C ALA* 3.3 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1002 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A THR* 4.1 6.4 + - - +
491A ILE* 3.9 21.8 - - + +
463C GLN* 4.0 18.2 - - - -
465C ALA* 3.8 23.3 - - + -
466C VAL* 3.4 40.8 - - + -
469C ALA* 4.3 7.6 - - + -
998C TYR* 3.7 45.7 + + - -
999C LEU* 3.1 11.3 + - - +
1001C LYS* 1.3 80.0 - - + +
1003C MET* 1.3 64.3 + - + +
1005C ALA* 3.0 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1003 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LYS* 4.3 25.8 - - + +
484A MET 5.3 0.4 - - - +
486A ARG* 4.5 7.4 + - - +
487A THR* 3.4 33.8 + - - +
469C ALA* 3.5 33.9 - - + +
470C ILE* 3.9 13.5 - - + -
473C ASN* 3.9 35.7 - - + +
474C THR* 5.4 2.5 - - + -
999C LEU* 3.0 19.4 + - + +
1000C GLN* 3.1 8.9 + - - +
1002C PHE* 1.3 75.9 - - - +
1004C ASN* 1.3 61.1 + - - +
1005C ALA 3.4 1.0 + - - -
1006C HIS* 4.0 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1004 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ARG* 5.9 0.8 - - - +
1000C GLN* 3.0 21.6 + - - +
1001C LYS* 3.0 14.0 + - - +
1003C MET* 1.3 81.0 + - - +
1005C ALA* 1.3 63.1 + - - +
1006C HIS* 2.8 13.4 + - - -
1007C ASN* 2.9 36.5 + - + +
----------------------------------------------------------
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