Contacts of the helix formed by residues 1005 - 1010 (chain C) in PDB entry 7C97
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 GLU1005 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981C ALA* 5.5 1.2 - - - +
982C GLY 5.6 0.3 + - - -
1003C THR* 2.6 34.8 + - - +
1004C ASP* 1.3 79.9 - - - +
1006C GLU* 1.3 63.6 + - - +
1007C LYS* 2.4 49.1 + - + +
1008C GLN* 3.0 2.1 + - - +
1009C ASN* 2.7 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1006 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978C VAL* 4.7 11.8 - - + +
1005C GLU* 1.3 78.4 - - - +
1007C LYS* 1.3 69.5 + - - +
1009C ASN* 3.6 14.0 - - + +
1010C GLN* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1007 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978C VAL* 3.3 41.0 - - + +
979C LEU* 3.0 28.4 - - + +
981C ALA* 4.5 15.5 - - - -
982C GLY 4.6 0.4 - - - +
1002C LEU* 3.3 24.5 - - + -
1003C THR* 3.8 18.2 - - - +
1005C GLU* 2.4 44.9 + - + +
1006C GLU* 1.3 93.4 + - - +
1008C GLN* 1.3 65.3 + - - +
1010C GLN* 3.5 7.1 + - - +
1011C LEU* 3.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1008 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C LEU* 3.2 17.9 - - - +
1003C THR 2.9 24.5 - - - +
1004C ASP* 2.3 36.3 + - - +
1005C GLU 3.0 16.5 + - - +
1007C LYS* 1.3 76.0 - - - +
1009C ASN* 1.3 83.1 + - - +
1010C GLN 3.1 2.2 - - - -
1011C LEU* 3.0 30.7 + - + +
1012C GLU* 3.9 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1009 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004C ASP 4.5 0.5 - - - -
1005C GLU* 2.7 37.3 + - - +
1006C GLU* 3.3 12.0 + - + +
1008C GLN* 1.3 94.9 + - - +
1010C GLN* 1.3 55.2 + - - +
1012C GLU* 5.5 0.4 - - - +
1013C GLN* 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1010 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C PRO 4.4 4.4 + - - -
744C GLY* 3.8 10.7 - - - -
745C GLU* 2.8 50.2 + - - +
971C LEU* 4.2 4.7 - - - +
974C ARG* 4.2 13.9 + - - +
975C ILE* 3.3 31.4 - - + +
978C VAL* 5.9 1.6 - - + -
1006C GLU* 2.8 17.4 + - - +
1007C LYS* 3.7 7.0 - - - +
1008C GLN 3.1 0.6 - - - -
1009C ASN* 1.3 78.7 + - - +
1011C LEU* 1.3 58.1 + - - +
1013C GLN* 3.4 7.6 - - - +
1014C LEU* 2.9 30.5 + - + +
----------------------------------------------------------
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