Contacts of the helix formed by residues 4193 - 4201 (chain H) in PDB entry 6X34
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 SER4193 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4172H TYR* 5.0 0.8 - - - -
4191H GLU 4.0 2.6 + - - -
4192H ILE* 1.3 84.4 - - - +
4194H GLU* 1.3 63.0 + - - +
4195H THR* 3.5 9.8 + - - +
4196H ASN* 3.0 27.9 + - - +
4197H ARG* 3.4 15.4 + - - +
4991H MET* 5.2 5.4 - - - +
4995H ASN* 6.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4172H TYR* 4.0 27.5 - - + +
4192H ILE 3.7 1.4 + - - -
4193H SER* 1.3 72.3 - - - +
4195H THR* 1.3 63.0 + - - +
4197H ARG* 3.6 4.4 + - - +
4198H ALA* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR4195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4193H SER* 3.2 8.3 + - - +
4194H GLU* 1.3 81.2 - - - +
4196H ASN* 1.3 65.0 + - + +
4198H ALA* 3.5 5.8 + - - +
4199H GLN* 3.3 21.1 + - - +
4991H MET* 6.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4192H ILE* 5.0 1.5 - - + +
4193H SER* 3.0 22.7 + - - +
4195H THR* 1.3 80.0 - - + +
4197H ARG* 1.3 65.1 + - - +
4199H GLN* 3.4 6.7 + - - +
4200H TRP* 3.2 27.0 + - - +
4237H ILE* 4.8 4.4 - - - +
4987H MET* 4.4 4.7 + - - +
4988H PHE* 3.2 34.8 + - + +
4991H MET* 3.6 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4171H PRO 5.9 2.2 - - - +
4172H TYR* 5.6 7.0 - - + -
4192H ILE* 4.8 9.6 - - + +
4193H SER 3.4 13.9 + - - +
4194H GLU* 4.1 7.2 - - - +
4195H THR 3.4 0.4 - - - -
4196H ASN* 1.3 80.1 + - - +
4198H ALA* 1.3 61.7 + - - +
4200H TRP* 3.4 17.8 + - - +
4201H GLU* 3.7 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4194H GLU 3.3 15.3 + - - +
4195H THR* 3.9 6.7 - - - +
4196H ASN 3.3 0.8 - - - -
4197H ARG* 1.3 80.8 - - - +
4199H GLN* 1.3 59.0 + - - +
4201H GLU* 3.4 21.0 + - - +
4202H MET* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4195H THR* 3.3 14.8 + - + +
4196H ASN* 3.4 8.5 + - - +
4197H ARG 3.4 0.2 - - - -
4198H ALA* 1.3 77.2 - - - +
4200H TRP* 1.3 64.2 - - - +
4201H GLU 3.2 0.4 + - - -
4202H MET* 3.5 20.5 - - - +
4205H VAL* 3.5 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP4200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4196H ASN* 3.2 18.9 + - - +
4197H ARG* 3.6 13.0 - - - +
4198H ALA 3.2 0.8 - - - -
4199H GLN* 1.3 78.5 - - - +
4201H GLU* 1.3 57.9 + - + +
4202H MET 3.2 6.4 + - - +
4205H VAL* 3.3 24.0 - - + +
4206H LYS* 5.1 3.6 + - - +
4209H LYS* 5.4 14.6 - - + -
4232H PHE* 5.9 7.4 - + - -
4236H THR* 6.0 5.4 - - + -
4984H ALA* 4.9 8.2 - - + +
4985H ASN* 4.1 34.0 - - + +
4986H TYR 5.4 0.4 - - - -
4987H MET* 4.3 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4197H ARG 3.7 7.2 + - - +
4198H ALA* 3.4 15.4 + - - +
4199H GLN 3.2 0.8 - - - -
4200H TRP* 1.3 76.7 - - + +
4202H MET* 1.3 58.4 + - - +
4203H PRO* 4.6 1.7 - - - +
4206H LYS* 6.3 0.2 - - - -
----------------------------------------------------------
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