Contacts of the helix formed by residues 4154 - 4162 (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 GLY4154 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4122D TYR* 3.4 32.5 - - - -
4152D TYR 3.7 1.4 + - - -
4153D ASP* 1.3 74.9 + - - +
4155D LEU* 1.3 64.4 + - - +
4156D ALA 3.4 1.1 - - - -
4157D LEU* 3.5 3.3 + - - -
4158D ALA* 3.0 26.9 + - - +
4165D VAL* 4.0 18.4 - - - +
4167D THR* 5.4 0.4 - - - +
4476D PHE* 4.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4038D VAL* 4.0 33.0 - - + +
4039D SER 4.8 0.7 - - - +
4040D LEU* 4.0 36.6 - - + -
4047D VAL* 3.5 36.1 - - + +
4049D ILE* 4.6 5.8 - - + -
4122D TYR* 3.5 10.4 - - + -
4153D ASP* 3.0 20.6 + - - +
4154D GLY* 1.3 76.6 - - - +
4156D ALA* 1.3 58.2 + - - +
4158D ALA* 3.8 3.0 - - - +
4159D ALA* 2.9 32.2 + - - +
4481D LEU* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D LEU* 3.8 20.6 - - + -
4153D ASP 4.7 1.6 + - - -
4154D GLY 3.4 0.4 - - - -
4155D LEU* 1.3 76.3 - - - +
4157D LEU* 1.3 61.2 + - - +
4160D HIS* 2.9 41.3 + - + +
4476D PHE 3.9 17.5 - - - +
4477D GLY* 3.9 19.3 - - - +
4480D PHE* 4.5 4.3 - - + -
4481D LEU* 4.4 13.3 - - + +
4497D MET* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4136D MET* 4.4 14.1 - - + -
4154D GLY* 3.5 9.9 + - - +
4155D LEU 3.4 0.4 - - - -
4156D ALA* 1.3 78.0 - - - +
4158D ALA* 1.3 64.1 + - - +
4161D GLU* 3.0 37.7 + - + +
4163D VAL* 4.1 6.6 - - + +
4165D VAL* 3.9 21.1 - - + -
4218D PHE* 4.2 27.4 - - + -
4475D VAL* 4.1 20.9 - - + +
4476D PHE* 4.7 13.2 + - + -
4497D MET* 3.9 37.3 - - + +
4500D TRP* 5.5 3.4 - - + -
4501D ALA* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4047D VAL* 4.6 6.1 - - + -
4122D TYR* 3.7 22.2 - - + +
4124D PRO* 3.4 15.6 - - + +
4154D GLY 3.0 18.9 + - - +
4155D LEU 3.8 2.9 - - - +
4157D LEU* 1.3 78.8 - - - +
4159D ALA* 1.3 56.9 + - - +
4162D ASN* 2.9 28.9 + - - -
4163D VAL* 3.3 23.8 - - - +
4165D VAL* 3.9 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D LEU* 3.9 25.4 - - + -
4043D PHE* 3.5 27.8 - - + -
4045D GLN 5.6 2.0 - - - +
4047D VAL* 4.1 17.9 - - + +
4124D PRO* 4.6 4.6 - - - +
4155D LEU 2.9 18.4 + - - +
4157D LEU 3.3 0.2 - - - -
4158D ALA* 1.3 77.2 - - - +
4160D HIS* 1.3 65.7 + - - +
4162D ASN* 4.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS4160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D LEU* 3.6 15.7 - - + +
4043D PHE* 3.4 39.0 - + - -
4156D ALA* 2.9 31.4 + - + +
4157D LEU 4.3 0.9 - - - +
4159D ALA* 1.3 75.6 - - - +
4161D GLU* 1.3 73.3 + - + +
4162D ASN* 5.4 0.2 - - - +
4480D PHE* 3.8 41.9 - + - -
4494D LYS* 4.8 11.5 - - + -
4497D MET* 3.8 24.6 - - + +
4498D LYS* 4.8 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4157D LEU* 3.0 19.6 + - + +
4160D HIS* 1.3 86.7 - - + +
4162D ASN* 1.3 71.2 + - - +
4163D VAL* 3.4 5.1 - - + +
4494D LYS 4.6 1.9 - - - +
4497D MET* 3.6 21.9 - - + +
4498D LYS* 2.9 49.9 + - - +
4501D ALA* 3.4 23.6 - - + -
4505D ARG* 2.9 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4124D PRO* 3.8 22.8 - - - +
4125D ALA* 5.5 0.2 - - - -
4133D LEU* 3.4 38.7 - - - +
4134D PRO* 4.1 4.7 - - - +
4158D ALA 2.9 13.5 + - - -
4159D ALA 4.0 3.8 + - - +
4160D HIS 3.6 2.0 - - - +
4161D GLU* 1.3 80.9 - - - +
4163D VAL* 1.3 61.8 + - - +
4505D ARG* 4.6 2.4 + - - +
----------------------------------------------------------
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