Contacts of the helix formed by residues 4172 - 4178 (chain D) in PDB entry 2H7C
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 LEU4172 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4087D CYS* 4.1 15.6 - - + +
4088D THR 4.4 7.7 - - - +
4089D GLN* 3.5 28.0 - - + +
4140D HIS* 4.1 4.0 - - + +
4144D LEU* 3.6 20.2 - - - +
4145D MET 3.8 8.3 - - - +
4146D VAL* 3.6 26.9 - - - +
4147D GLY 3.7 7.2 - - - +
4170D TYR* 3.4 45.5 - - + +
4171D ARG* 1.3 74.2 - - - +
4173D GLY* 1.3 69.4 + - - +
4174D ILE 3.5 0.3 + - - -
4175D TRP* 3.2 18.3 + - - +
4176D GLY* 3.0 9.5 + - - -
4177D PHE* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4088D THR 5.8 0.2 - - - -
4144D LEU 2.8 15.7 + - - -
4145D MET* 3.6 34.3 - - - +
4172D LEU* 1.3 72.4 - - - +
4174D ILE* 1.3 54.8 + - - -
4175D TRP* 4.9 2.9 - - - -
4176D GLY 3.2 0.2 + - - -
4177D PHE* 2.8 38.1 + - - +
4298D THR* 6.2 0.4 - - - -
4319D LEU* 3.8 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4065D PHE* 3.3 23.4 - - + -
4145D MET* 5.0 0.8 - - - +
4172D LEU 3.5 0.6 + - - -
4173D GLY* 1.3 70.1 - - - -
4175D TRP* 1.3 74.4 + - + +
4178D PHE* 3.0 40.0 + - + +
4268D ILE* 4.1 15.3 - - + -
4286D LEU* 5.6 0.9 - - + -
4294D LEU* 3.8 29.6 - - + +
4297D THR* 3.9 22.7 - - + -
4298D THR* 3.5 25.3 + - + +
4301D MET* 5.5 0.2 - - + -
4303D PHE* 4.8 7.2 - - + -
4319D LEU* 3.6 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP4175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4059D PRO 6.0 1.6 - - - -
4064D ARG* 4.1 20.3 - - + +
4065D PHE* 4.2 11.7 + - - -
4087D CYS* 6.5 0.7 - - + -
4088D THR* 3.3 53.8 - - + -
4089D GLN* 4.8 2.9 - - - -
4114D GLU* 2.9 37.7 + - + +
4171D ARG* 3.6 29.7 + - + -
4172D LEU 3.5 15.3 - - - +
4173D GLY* 3.2 1.9 - - - -
4174D ILE* 1.3 86.4 - - + +
4176D GLY* 1.3 59.2 + - - +
4189D TRP* 3.6 13.2 - - - +
4291D GLU* 3.7 9.6 - - + -
4294D LEU* 3.4 33.0 - - + +
4295D LEU* 3.8 20.2 - - + -
4298D THR* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4171D ARG* 3.4 31.4 - - - +
4172D LEU 3.0 10.3 + - - -
4173D GLY 3.8 1.1 - - - -
4175D TRP* 1.3 77.7 - - - +
4177D PHE* 1.3 68.8 + - - +
4189D TRP* 2.9 15.6 + - - -
4190D GLY 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4144D LEU* 3.7 47.3 - - + -
4170D TYR* 4.7 3.8 - + - -
4171D ARG 3.5 19.3 - - - -
4172D LEU* 4.4 0.2 - - - -
4173D GLY 2.8 23.5 + - - +
4176D GLY* 1.3 83.4 - - - +
4178D PHE* 1.3 67.4 + - - +
4179D SER* 3.2 10.1 + - - -
4187D GLY* 4.7 0.9 - - - -
4188D ASN* 4.0 16.1 + - - +
4189D TRP* 4.4 1.6 - - - -
4190D GLY* 3.8 15.3 - - - -
4191D HIS* 3.5 35.2 - + - -
4319D LEU* 3.9 24.5 - - + +
4320D GLY 3.6 30.5 + - - +
4321D THR 4.1 0.2 - - - -
4322D VAL* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4065D PHE* 3.6 22.0 - + + -
4173D GLY 4.0 0.2 + - - -
4174D ILE* 3.0 26.9 + - + +
4176D GLY 3.9 0.2 - - - -
4177D PHE* 1.3 74.6 - - - +
4179D SER* 1.3 59.9 + - - +
4180D THR* 3.7 23.3 - - + -
4185D SER* 3.2 17.3 + - - -
4187D GLY* 3.6 3.1 - - - -
4189D TRP* 3.1 21.8 + - - -
4265D ALA* 3.8 42.4 - - + -
4268D ILE* 4.0 25.8 - - + -
4282D MET* 4.9 6.7 - - + -
4283D VAL* 4.0 11.9 - - + -
4286D LEU* 3.3 34.3 - - + -
4319D LEU* 4.9 3.8 - - - -
----------------------------------------------------------
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