Contacts of the helix formed by residues 4054 - 4058 (chain D) in PDB entry 4O2W
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 GLY4054 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4052D GLY 3.4 1.6 + - - -
4053D GLU* 1.3 73.2 - - - +
4055D SER* 1.3 71.0 + - - +
4057D GLY 3.1 13.0 + - - -
4058D ARG* 3.9 0.7 - - - -
4059D LEU* 3.9 2.2 - - - -
4064D SER* 3.3 12.8 - - - -
4065D ASP 3.4 21.5 - - - -
4066D ASP* 2.8 10.9 + - - -
4405D UNX 3.1 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER4055 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4053D GLU* 2.6 32.4 + - - +
4054D GLY* 1.3 79.7 - - - +
4056D TYR* 1.3 83.9 + - - +
4058D ARG* 3.2 24.7 + - - +
4064D SER* 3.6 7.1 + - - -
4066D ASP* 4.3 0.2 + - - -
4407D UNX 4.2 12.5 + - - -
4409D UNX 3.5 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4056 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4132A GLN* 5.7 2.1 + - - +
4133A GLY* 3.4 38.3 - - - -
4055D SER* 1.3 87.1 - - - +
4057D GLY* 1.3 59.2 + - - +
4058D ARG* 3.4 3.5 + - - -
4064D SER* 3.4 2.6 + - - -
4091D ASP* 3.4 56.8 + - + +
4092D GLY 4.7 0.2 - - - +
4107D GLY* 3.3 23.4 - - - +
4108D ASP* 3.7 17.2 - - + +
4121D ARG* 3.4 36.9 - - - +
4122D GLN 5.0 0.3 - - - +
4409D UNX 2.9 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4057 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4054D GLY 3.1 4.6 + - - -
4056D TYR* 1.3 75.6 - - - +
4058D ARG* 1.3 64.6 + - - +
4060D GLY* 3.1 13.9 + - - -
4063D ASN 3.7 9.4 - - - -
4064D SER* 3.3 7.6 + - - -
4106D TRP* 3.6 9.2 - - - -
4107D GLY* 4.0 5.4 + - - -
4122D GLN 4.2 2.6 - - - +
4123D ARG* 4.2 19.7 - - - +
4405D UNX 3.2 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4058 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4036D GLN* 2.8 51.0 + - - +
4038D CYS* 3.6 32.3 - - - -
4040D PHE* 3.6 9.1 - - + -
4053D GLU* 3.3 44.8 + - - +
4054D GLY 3.1 1.0 + - - -
4055D SER* 3.2 29.8 + - - +
4056D TYR* 3.3 6.2 - - - -
4057D GLY* 1.3 76.8 - - - +
4059D LEU* 1.3 57.1 + - - +
4060D GLY 3.3 0.2 - - - -
4086D THR* 5.3 2.0 - - - +
4090D SER 4.5 0.2 + - - -
4091D ASP* 3.0 30.7 + - - +
4092D GLY* 4.1 12.5 - - - -
4093D HIS* 6.1 1.0 - - - +
4094D SER* 4.2 6.6 + - - +
4106D TRP* 2.9 21.6 + - - +
4107D GLY* 4.8 5.2 - - - -
4405D UNX 3.1 3.2 + - - -
----------------------------------------------------------
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