Contacts of the strand formed by residues 130 - 133 (chain T) in PDB entry 2A3W
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 LYS 130 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T ASN* 5.6 11.9 - - + +
53T ASN 2.8 21.0 + - - +
129T PRO* 1.3 73.1 - - - +
131T ILE* 1.3 62.6 + - - +
132T VAL* 4.8 2.5 - - + -
137T GLN* 2.8 39.2 + - - +
140T TYR* 3.6 40.3 + - + -
141T GLY* 3.9 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T ASN* 3.5 2.3 - - - +
22T LEU* 2.7 59.1 + - + +
24T THR* 3.7 31.0 - - + -
50T PHE* 3.5 33.7 - - + -
51T SER 3.3 7.0 - - - +
52T TYR* 3.7 29.8 - - + -
129T PRO* 3.9 8.7 - - + +
130T LYS* 1.3 76.3 - - - +
132T VAL* 1.3 66.0 + - - +
159T MET* 5.3 2.9 - - - -
182T ILE* 5.4 0.2 - - + -
183T LEU* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T HIS* 4.2 10.8 - - + -
20T VAL 3.3 5.6 - - - +
21T ASN* 3.2 26.7 - - - +
22T LEU 4.8 0.2 - - - +
48T SER* 5.3 0.2 + - - -
49T LEU 5.2 0.2 - - - -
50T PHE* 4.1 0.7 - - - -
51T SER* 2.8 38.1 + - - -
130T LYS* 4.8 3.4 - - + -
131T ILE* 1.3 78.5 - - - +
133T LEU* 1.3 69.0 + - - +
135T GLN* 3.3 25.8 - - + +
137T GLN* 3.4 38.6 - - + +
141T GLY* 4.6 8.1 - - - +
144T PHE* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T PHE* 4.1 24.0 - - + -
11T PHE* 3.6 14.3 - - + -
19T HIS* 3.3 8.1 - - - +
20T VAL* 2.9 34.4 + - + +
22T LEU* 3.7 41.7 - - + -
49T LEU 3.9 11.4 - - - +
50T PHE* 3.9 21.3 - - + -
131T ILE* 5.0 0.2 - - + -
132T VAL* 1.3 79.0 - - - +
134T GLY* 1.3 56.8 - - - +
135T GLN 3.3 4.5 - - - -
154T ILE* 4.2 26.5 - - + -
157T LEU* 4.7 8.5 - - + -
185T TRP* 5.1 1.6 - - + -
----------------------------------------------------------
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