Contacts of the helix formed by residues 695 - 705 (chain N) in PDB entry 2VUU
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 695 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F SER* 3.2 26.5 + - - -
327F GLY* 3.4 15.6 - - - -
681N THR* 3.0 16.2 + - - +
682N PRO* 4.2 18.1 - - + +
683N LEU* 3.1 32.4 + - - +
685N ARG* 2.7 39.0 + - - +
694N CYS* 1.3 72.3 - - - +
696N ALA* 1.3 56.6 + - - +
699N LEU* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 696 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F HIS* 3.6 22.7 - - + +
325F TRP* 3.9 3.7 - - + -
327F GLY* 3.4 30.9 - - - +
694N CYS* 3.2 9.9 - - - +
695N ASN* 1.3 76.3 - - - +
697N CYS* 1.3 67.4 + - - +
699N LEU* 3.1 2.1 + - - +
700N PHE* 2.8 26.2 + - - +
708N ARG* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 697 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673N CYS* 3.3 11.7 - - - -
675N ASN* 3.5 27.4 - - + +
676N CYS* 3.3 8.1 - - - -
693N LEU* 4.3 9.3 - - + +
694N CYS* 3.0 15.6 - - - +
696N ALA* 1.3 72.0 - - - +
698N GLY* 1.3 62.7 + - - +
700N PHE* 3.8 1.2 - - - +
701N LEU* 3.0 25.8 + - - +
707N VAL* 5.5 0.2 - - - -
708N ARG* 3.6 24.6 + - - +
1713N ZN 2.1 38.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 698 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685N ARG* 3.4 23.9 + - - -
693N LEU* 3.9 19.6 - - - +
694N CYS 3.0 10.8 + - - -
697N CYS* 1.3 77.5 - - - +
699N LEU* 1.3 56.7 + - - +
701N LEU* 3.6 3.4 + - - +
702N LYS* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 699 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325F TRP* 3.8 12.6 - - + -
326F SER* 3.0 30.7 - - - +
327F GLY* 3.4 22.2 - - - +
685N ARG* 3.3 25.6 - - - +
695N ASN* 2.8 24.0 + - - +
696N ALA 3.5 2.9 - - - +
698N GLY* 1.3 73.5 - - - +
700N PHE* 1.3 59.7 + - - +
702N LYS* 3.2 15.4 + - + +
703N LEU* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 700 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F VAL* 3.3 28.3 - - + -
28F VAL* 3.7 23.3 - - + -
198F PRO* 4.5 12.1 - - + -
325F TRP* 4.0 10.5 - + + -
696N ALA 2.8 20.2 + - - +
697N CYS 3.8 3.1 - - - +
699N LEU* 1.3 71.7 - - - +
701N LEU* 1.3 65.5 + - - +
703N LEU* 3.3 4.8 + - - -
704N HIS* 2.8 42.8 + + + +
706N VAL* 3.1 43.5 - - + -
708N ARG* 3.4 39.9 - - + -
709N PRO* 3.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 701 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687N ASN* 4.4 11.4 - - - +
688N PRO* 6.5 0.9 - - + -
693N LEU* 4.2 22.0 - - + -
697N CYS 3.0 14.9 + - - +
698N GLY 3.8 4.5 - - - +
700N PHE* 1.3 78.2 - - - +
702N LYS* 1.3 60.6 + - - +
705N GLY* 2.7 47.8 + - - +
706N VAL* 3.1 33.2 - - - +
707N VAL* 3.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 702 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685N ARG* 4.6 15.7 - - - +
698N GLY 3.0 15.2 + - - +
699N LEU* 3.3 24.5 - - + +
700N PHE 3.2 0.2 - - - -
701N LEU* 1.3 79.3 - - - +
703N LEU* 1.3 70.6 + - + +
705N GLY* 4.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 703 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F GLN* 5.1 7.2 - - - +
205F LYS* 4.1 22.4 + - - +
325F TRP* 3.8 19.1 - - + -
699N LEU* 2.9 51.0 + - + +
700N PHE* 4.0 2.9 - - - +
702N LYS* 1.3 85.5 - - + +
704N HIS* 1.3 70.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 704 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 5.8 2.8 - - - -
28F VAL* 3.8 30.9 - - + +
198F PRO* 5.3 4.0 + - - +
201F LEU* 3.9 29.7 - - + +
202F GLN* 5.0 2.6 + - + -
205F LYS* 3.1 39.7 + - - -
325F TRP* 5.3 4.0 - - - -
700N PHE* 2.8 54.8 + + + +
702N LYS 4.8 0.2 - - - -
703N LEU* 1.3 85.5 + - + +
705N GLY* 1.3 58.6 + - - +
706N VAL* 3.4 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 705 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701N LEU* 2.7 34.5 + - - +
702N LYS 4.2 1.9 + - - -
703N LEU 3.8 0.8 - - - -
704N HIS* 1.3 73.1 - - - +
706N VAL* 1.3 64.3 + - - +
----------------------------------------------------------
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