Contacts of the helix formed by residues 2192 - 2198 (chain F) in PDB entry 5G1N
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 SER2192 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2166F ILE* 5.1 2.3 - - - +
2167F LEU 2.9 20.0 + - - -
2168F THR* 3.9 20.0 - - - -
2169F PRO* 3.7 5.5 - - - +
2187F ARG* 3.6 0.5 + - - -
2189F ASN 4.3 3.3 + - - -
2190F GLU 4.3 0.4 - - - -
2191F ILE* 1.3 75.7 - - - +
2193F VAL* 1.3 63.6 + - - +
2194F GLU* 2.9 29.5 + - - +
2195F VAL* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008D ALA* 6.5 0.7 - - + -
2187F ARG* 3.7 11.7 - - - +
2191F ILE 3.4 2.6 + - - -
2192F SER* 1.3 70.5 + - - +
2194F GLU* 1.3 66.5 + - + +
2196F ASP* 2.7 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2169F PRO* 3.4 30.1 - - + +
2192F SER* 2.9 10.8 + - - +
2193F VAL* 1.3 87.1 - - + +
2195F VAL* 1.3 60.9 + - - +
2196F ASP 3.3 0.3 + - - -
2197F SER* 3.5 19.9 + - - -
2198F ASP* 4.4 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167F LEU* 3.7 31.9 - - + +
2168F THR 4.2 14.8 - - - -
2169F PRO* 4.3 6.0 - - + +
2172F MET* 5.0 8.5 - - + -
2181F VAL* 4.4 9.6 - - + -
2191F ILE* 3.7 10.5 - - + -
2192F SER* 3.0 22.4 + - - +
2194F GLU* 1.3 78.6 - - - +
2196F ASP* 1.3 61.9 + - - +
2197F SER 2.9 2.4 + - - -
2198F ASP* 3.2 25.1 + - + +
2201F ALA* 3.6 14.4 - - + +
2203F TYR* 3.3 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009D ASP* 4.8 0.2 - - - +
2012D GLN* 4.7 5.2 + - - +
2187F ARG* 2.8 45.4 + - - -
2192F SER 3.8 0.2 - - - +
2193F VAL* 2.7 39.6 + - + +
2195F VAL* 1.3 69.0 - - - +
2197F SER* 1.3 58.4 + - - +
2198F ASP 3.9 5.2 - - - +
2201F ALA* 4.5 5.2 - - - +
2203F TYR* 3.0 20.4 + - + -
2204F PHE* 4.4 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2194F GLU 3.5 11.9 + - - -
2195F VAL 2.9 3.6 + - - -
2196F ASP* 1.3 73.1 - - - +
2198F ASP* 1.3 70.4 + - - +
2199F PRO* 3.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172F MET* 3.7 17.1 - - - +
2194F GLU 4.4 0.9 + - - +
2195F VAL* 3.2 18.7 + - + +
2196F ASP 3.9 2.4 - - - +
2197F SER* 1.3 81.7 + - - +
2199F PRO* 1.3 76.0 - - - +
2200F ARG* 2.9 54.9 + - - +
2201F ALA* 3.2 22.3 + - + +
----------------------------------------------------------
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