Contacts of the helix formed by residues 576 - 586 (chain B) in PDB entry 6QVC
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 576 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 6.0 0.2 + - - -
366B VAL* 3.6 2.2 - - - +
536B VAL 4.5 0.8 + - - -
537B SER 4.5 4.7 + - - -
538B HIS* 3.3 34.1 + - - +
575B PRO* 1.3 78.0 - - - +
577B LEU* 1.3 70.6 + - - +
578B TYR* 3.3 16.5 + - - +
579B ASP* 3.3 32.9 + - - +
580B SER* 2.7 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 5.1 10.5 - - + -
366B VAL* 4.0 19.6 - - + +
369B HIS* 4.4 22.7 - - + +
483B GLY* 4.3 21.3 - - - +
536B VAL* 3.8 31.9 + - + +
537B SER* 5.3 1.3 - - - -
575B PRO 3.9 0.2 + - - -
576B SER* 1.3 75.8 + - - +
578B TYR* 1.3 92.7 + - + +
580B SER* 3.2 7.1 + - - -
581B ILE* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY* 6.0 0.9 - - - -
191B ILE* 3.5 34.4 - - + +
192B PRO* 3.6 33.3 - - + +
195B LYS* 5.0 6.5 - - + +
232B GLU* 3.4 22.2 + - - -
233B GLY* 5.8 0.6 - - - -
288B PHE* 5.5 8.6 - + - -
481B CYS 6.0 1.3 - - - -
483B GLY* 3.8 17.9 + - - -
537B SER* 5.3 17.7 - - - -
576B SER* 3.3 9.1 + - - +
577B LEU* 1.3 98.2 - - + +
579B ASP* 1.3 62.4 + - - +
581B ILE* 3.2 18.9 + - + +
582B ILE* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 3.6 24.9 + - - +
575B PRO* 5.0 4.7 - - + -
576B SER* 3.3 30.5 + - - +
577B LEU 3.2 0.4 - - - -
578B TYR* 1.3 76.5 - - - +
580B SER* 1.3 59.5 + - - +
582B ILE* 3.3 18.1 - - + +
583B GLN* 2.9 29.5 + - - +
589B TYR* 5.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B VAL* 3.8 10.7 - - - +
369B HIS* 5.8 4.9 - - - -
370B ARG* 4.0 25.0 + - - -
575B PRO* 3.3 23.4 - - - +
576B SER 2.7 20.6 + - - -
577B LEU 3.2 5.5 + - - -
579B ASP* 1.3 78.4 - - - +
581B ILE* 1.3 58.2 + - - +
583B GLN* 3.6 7.8 - - - +
584B VAL* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 4.1 17.7 - - + -
369B HIS* 4.2 22.4 - - + +
577B LEU* 2.9 35.4 + - + +
578B TYR* 3.4 33.0 - - + +
579B ASP 3.2 0.2 - - - -
580B SER* 1.3 77.1 - - - +
582B ILE* 1.3 60.2 + - + +
584B VAL* 3.8 3.1 - - - +
585B LYS* 2.8 46.7 + - + +
587B LEU* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 3.7 35.9 - - + +
195B LYS* 6.0 1.6 - - + -
196B THR* 4.1 8.3 - - - +
578B TYR 2.9 17.7 + - - +
579B ASP* 3.3 26.0 - - + +
581B ILE* 1.3 76.7 - - + +
583B GLN* 1.3 61.2 + - + +
585B LYS 4.5 0.4 - - - +
586B LYS* 3.0 21.0 + - - -
587B LEU* 3.3 44.5 + - + +
589B TYR* 4.1 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 4.3 14.1 - - - +
579B ASP 2.9 19.2 + - - +
580B SER* 3.6 7.5 + - - +
582B ILE* 1.3 82.4 - - + +
584B VAL* 1.3 84.7 + - - +
586B LYS* 3.2 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS* 6.6 0.2 - - + -
370B ARG* 4.2 19.5 - - + -
373B MET* 3.7 43.1 - - + +
374B LEU* 4.8 17.0 - - + +
580B SER 2.9 20.6 + - - +
581B ILE* 4.0 3.4 - - - +
583B GLN* 1.3 93.0 - - - +
585B LYS* 1.3 63.6 + - + +
586B LYS* 3.2 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 5.0 9.7 + - - +
188B GLY* 5.4 7.1 + - - -
373B MET* 4.6 19.5 - - + -
581B ILE* 2.8 33.8 + - + +
584B VAL* 1.3 76.1 - - + +
586B LYS* 1.3 72.4 - - - +
587B LEU* 3.5 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ILE 3.0 9.5 + - - -
583B GLN 3.2 12.5 + - - +
584B VAL* 3.1 16.5 - - - +
585B LYS* 1.3 80.9 - - - +
587B LEU* 1.3 62.0 + - - +
588B PRO* 4.3 2.9 - - - +
----------------------------------------------------------
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