Contacts of the helix formed by residues 67 - 78 (chain 7) in PDB entry 6CP3
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 VAL 67 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 LEU* 4.5 0.9 - - + -
657 THR 2.6 19.7 + - - +
667 SER* 1.3 84.1 - - - +
687 ILE* 1.3 67.6 + - + +
697 ASP 3.3 2.9 - - - -
707 LYS* 3.0 13.6 + - + +
717 ILE* 2.8 39.4 + - + +
154Z LEU* 5.0 0.7 - - + -
157Z TRP* 3.5 58.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 VAL* 4.0 12.8 - - + -
587 TYR 4.2 1.3 - - - +
597 ARG* 3.6 40.8 - - + +
627 LEU* 3.7 34.1 - - + -
657 THR* 3.7 26.1 + - + +
677 VAL* 1.3 79.8 - - + +
697 ASP* 1.3 57.2 + - - +
717 ILE* 3.8 6.1 - - + +
727 GLU* 2.8 32.0 + - - +
154Z LEU* 3.6 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 ARG* 4.9 7.9 - - - +
657 THR* 4.7 6.3 - - + +
667 SER 5.3 1.5 - - - -
677 VAL 3.3 0.6 - - - +
687 ILE* 1.3 79.2 - - - +
707 LYS* 1.3 56.4 + - - +
727 GLU* 3.8 11.7 - - - +
737 SER* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576 ASN 4.8 3.2 + - - -
586 VAL* 4.4 34.1 + - - +
667 SER 4.8 4.0 - - - +
677 VAL* 3.0 22.8 + - + +
697 ASP* 1.3 78.5 - - - +
717 ILE* 1.3 72.2 + - + +
737 SER* 3.2 8.0 + - - -
747 TYR* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576 ASN 4.3 9.4 - - - +
596 GLU* 3.3 36.8 - - - +
537 VAL* 4.8 10.8 - - + -
677 VAL* 2.8 31.0 + - + +
687 ILE* 3.8 9.0 - - + +
707 LYS* 1.3 85.5 - - + +
727 GLU* 1.3 62.4 + - - +
747 TYR* 3.5 7.2 - - + +
757 VAL* 2.9 34.2 + - + +
150Z ALA* 4.6 6.3 - - + +
153Z VAL* 4.7 4.7 - - + -
154Z LEU* 4.4 33.2 - - + -
157Z TRP* 5.6 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 GLU* 5.9 1.0 - - - +
537 VAL* 3.3 44.8 + - - +
557 PHE* 4.4 20.5 - - + +
597 ARG* 5.9 2.0 - - - -
687 ILE* 2.8 22.8 + - + +
697 ASP* 3.5 15.5 - - - +
707 LYS 3.2 0.2 - - - -
717 ILE* 1.3 77.2 - - - +
737 SER* 1.3 58.0 + - - +
757 VAL* 3.3 8.0 + - - +
767 LYS* 2.9 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 ASP* 2.9 20.9 + - - -
707 LYS* 3.2 6.5 + - - -
727 GLU* 1.3 77.1 - - - +
747 TYR* 1.3 57.3 + - - +
767 LYS* 3.7 7.1 - - - +
777 GLN* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586 VAL* 3.2 27.1 + - + +
596 GLU* 3.2 26.9 - - + +
606 THR* 3.3 8.5 + - - -
616 ALA* 2.5 49.8 + - + +
707 LYS* 2.9 28.3 + - + +
717 ILE* 3.5 13.0 - - + +
727 GLU 3.2 0.2 - - - -
737 SER* 1.3 75.9 - - - +
757 VAL* 1.3 64.1 + - + +
777 GLN* 3.4 12.1 - - + +
787 TYR* 3.2 21.1 + - - +
146Z LEU* 4.7 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596 GLU* 4.8 6.1 - - - +
517 THR 4.7 14.6 - - - +
527 GLU* 5.1 8.5 - - + -
537 VAL* 4.8 10.1 - - + +
717 ILE 2.9 20.3 + - - +
727 GLU* 3.3 8.0 + - - +
747 TYR* 1.3 77.5 - - + +
767 LYS* 1.3 66.4 + - + +
787 TYR* 3.1 7.3 + - - -
797 LYS* 2.8 28.2 + - + -
146Z LEU* 4.9 17.5 - - + +
147Z ALA* 5.7 5.8 - - + -
150Z ALA* 4.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 GLU* 4.8 16.9 + - - +
557 PHE* 6.5 0.7 - - - -
727 GLU* 2.9 42.9 + - + +
737 SER* 4.1 6.7 - - - +
757 VAL* 1.3 79.2 - - + +
777 GLN* 1.3 65.5 + - - +
797 LYS* 3.4 54.8 - - + +
807 PRO* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737 SER 2.8 19.6 + - - +
747 TYR* 3.4 16.2 - - + +
767 LYS* 1.3 78.2 - - - +
787 TYR* 1.3 60.5 + - + +
797 LYS 3.2 3.7 + - - -
807 PRO* 3.6 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616 ALA* 3.5 31.4 - - + -
626 HIS 2.4 38.7 + - - -
636 VAL* 3.5 10.0 - - + +
747 TYR 3.2 8.6 + - - +
757 VAL 3.1 7.7 + - - +
777 GLN* 1.3 77.1 - - + +
797 LYS* 1.3 62.5 + - - +
807 PRO 3.5 5.6 - - - -
817 VAL* 3.2 57.7 + - + +
827 LYS* 4.3 2.9 - - - +
142Z GLN* 4.1 13.2 - - + +
143Z LYS* 6.3 0.2 - - - -
146Z LEU* 3.6 25.8 - - + +
----------------------------------------------------------
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