Contacts of the strand formed by residues 4136 - 4141 (chain B) 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 VAL4136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4097B LEU* 3.4 23.5 - - + +
4101B GLY* 3.3 24.1 + - - +
4103B VAL* 3.8 30.1 - - + -
4131B LEU* 4.5 13.2 - - + -
4134B GLU 4.4 5.4 - - - +
4135B GLU* 1.3 74.8 - - - +
4137B VAL* 1.3 64.3 + - - +
4138B GLN 3.8 16.2 - - - +
4139B MET* 4.0 6.5 - - + -
4148B VAL* 4.0 24.2 - - + -
4149B VAL 3.6 12.6 - - - +
4150B THR* 4.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083B GLN* 4.9 10.4 + - - +
4097B LEU* 3.9 15.4 - - - +
4135B GLU* 3.7 9.1 + - - +
4136B VAL* 1.3 76.9 - - - +
4138B GLN* 1.3 68.4 + - + +
4149B VAL* 2.9 21.1 + - + +
4150B THR 3.9 15.5 - - - +
4151B SER* 3.8 26.5 - - - +
4189B GLY 5.3 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083B GLN* 6.1 2.0 - - - -
4097B LEU* 5.2 0.4 - - - -
4136B VAL* 3.8 2.6 - - - +
4137B VAL* 1.3 83.7 - - + +
4139B MET* 1.3 89.7 + - - +
4140B SER* 4.7 0.2 - - - -
4148B VAL* 3.4 2.4 - - - -
4149B VAL* 2.9 36.3 + - + +
4189B GLY 4.4 11.2 - - - +
4190B GLN* 3.3 28.1 - - + +
4191B VAL* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083B GLN* 3.7 19.1 - - + +
4084B LEU 4.2 0.7 - - - +
4085B VAL* 3.5 27.8 - - + +
4095B MET* 3.5 50.9 - - + +
4097B LEU* 3.7 34.8 - - + +
4103B VAL* 4.1 17.7 - - - -
4136B VAL* 4.0 12.8 - - + -
4138B GLN* 1.3 101.2 + - - +
4140B SER* 1.3 62.8 + - - +
4147B ALA 3.4 8.1 - - - +
4148B VAL* 4.1 2.5 - - + +
4191B VAL* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER4140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4085B VAL* 4.1 5.8 - - - -
4095B MET* 3.5 9.6 - - - +
4139B MET* 1.3 79.1 - - - +
4141B CYS* 1.3 61.7 + - - +
4146B SER* 3.5 1.2 - - - -
4147B ALA 2.9 33.4 + - - +
4191B VAL* 3.6 22.2 - - - -
4192B ALA* 3.6 2.8 - - - +
4193B CYS* 3.0 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS4141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4085B VAL* 3.8 30.4 - - - +
4086B THR* 3.7 6.8 + - - +
4087B SER* 3.7 26.5 - - - +
4088B CYS 4.9 1.4 + - - -
4093B HIS* 3.6 41.5 - - + +
4094B SER 4.1 0.2 - - - -
4095B MET* 4.0 17.7 - - - -
4140B SER* 1.3 73.7 + - - +
4142B GLY* 1.3 60.5 + - - +
4145B HIS 3.9 3.6 - - - -
4146B SER* 4.6 0.2 - - - +
4193B CYS* 3.9 9.0 - - - +
----------------------------------------------------------
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