Contacts of the strand formed by residues 4090 - 4093 (chain D) in PDB entry 3CMT
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 CYS4090 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4080D ILE* 3.8 26.2 - - + -
4083D ALA* 4.0 12.6 - - - -
4084D GLN* 3.9 17.5 - - - +
4088D LYS 3.9 3.1 + - - -
4089D THR* 1.3 80.5 - - - +
4091D ALA* 1.3 60.8 + - - +
4113D ASN 4.1 4.1 + - - +
4114D LEU* 3.4 19.9 - - + +
4115D LEU* 3.0 27.8 + - - +
4138D VAL* 4.1 2.2 - - - -
4140D VAL* 3.2 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4091 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4080D ILE* 4.7 0.5 - - - +
4090D CYS* 1.3 74.1 - - - +
4092D PHE* 1.3 59.4 - - - +
4093D ILE* 4.2 4.7 - - + -
4114D LEU* 4.2 2.9 - - - -
4115D LEU* 3.2 17.0 - - + -
4132D LEU* 3.7 30.5 - - + -
4138D VAL* 3.9 11.2 - - + +
4140D VAL 2.9 6.8 + - - +
4141D ILE* 3.4 9.5 - - + -
4142D VAL* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4092 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4073D THR* 4.1 9.2 - - + -
4076D THR* 3.5 25.4 - - + -
4077D LEU* 4.0 14.6 - - + -
4080D ILE* 3.9 15.5 - - + -
4091D ALA* 1.3 73.8 - - - +
4093D ILE* 1.3 64.0 + - - +
4094D ASP* 3.6 35.5 + - + -
4099D LEU* 3.6 25.1 - - + -
4114D LEU* 3.8 22.9 - - + -
4115D LEU 2.7 8.7 + - - -
4116D CYS* 3.3 3.4 - - - -
4117D SER 2.9 24.8 + - - +
4142D VAL* 3.6 15.0 - - + -
4144D ASP* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4093 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4091D ALA* 4.9 1.3 - - + -
4092D PHE* 1.3 78.8 - - - +
4094D ASP* 1.3 58.6 + - - +
4095D ALA* 3.1 5.5 + - + +
4117D SER* 3.6 13.0 - - - +
4119D PRO* 3.8 30.7 - - + -
4125D ALA* 4.0 17.9 - - + +
4128D ILE* 3.9 28.3 - - + -
4129D CYS* 4.1 6.7 - - - -
4132D LEU* 4.6 6.5 - - + -
4141D ILE* 4.0 21.1 - - + -
4142D VAL 2.7 17.9 + - - +
4143D VAL* 3.6 17.6 - - + +
4144D ASP* 2.9 26.5 + - - +
----------------------------------------------------------
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