Contacts of the strand formed by residues 141 - 146 (chain B) in PDB entry 3TW4
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 CYS 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.6 4.0 - - + -
33B THR 3.8 2.7 + - - +
34B LEU* 3.5 23.2 - - + -
35B MET* 2.8 34.5 + - - +
139B VAL* 3.4 2.3 - - - +
140B GLN* 1.3 83.7 - - + +
142B CYS* 1.3 64.4 + - - +
143B LEU* 4.2 2.7 - - - -
168B VAL* 4.3 4.0 - - - -
169B ASN* 3.7 11.2 - - - -
171B ILE* 4.2 15.9 - - - -
204B TYR* 6.3 1.1 - - - -
278B LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET* 3.0 29.6 - - + +
37B VAL* 3.9 24.5 - - - -
141B CYS* 1.3 76.9 - - - +
143B LEU* 1.3 63.7 + - - +
144B TYR* 3.5 9.6 + - - -
168B VAL* 3.7 25.7 - - + +
169B ASN 2.8 11.2 + - - +
170B ILE* 3.7 9.3 - - + +
171B ILE 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.4 14.1 - - + +
35B MET 2.7 11.7 + - - +
36B VAL* 3.5 11.6 - - + -
37B VAL 2.9 26.0 + - - -
47B LEU* 6.3 0.7 - - + -
141B CYS* 4.0 4.4 - - - -
142B CYS* 1.3 71.0 - - - +
144B TYR* 1.3 56.4 + - - +
145B PHE* 3.3 16.5 - - + -
171B ILE* 3.4 15.9 - - + +
173B LEU* 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.0 41.3 - - + -
38B GLY* 5.3 1.8 - - - -
142B CYS* 3.5 7.8 + - - +
143B LEU* 1.3 72.6 - - - +
145B PHE* 1.3 71.0 + - - +
146B ILE* 3.3 26.9 - - + -
156B LEU* 4.4 6.2 + - - +
157B ASP* 3.1 42.5 + - + -
160B PHE* 3.9 21.9 - + + +
161B MET* 4.0 19.7 - - - -
170B ILE* 4.3 15.5 - - + -
171B ILE 2.9 10.7 + - - +
172B PRO* 3.2 10.3 - - + +
173B LEU* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.1 10.3 - - + -
37B VAL 2.9 22.8 + - - +
38B GLY* 4.3 4.0 - - - -
39B GLU 5.1 0.2 + - - -
42B LEU* 3.2 34.5 - - + +
43B GLY 5.2 0.4 - - - -
44B LYS* 3.0 48.7 - - + -
47B LEU* 3.6 26.9 - - + -
143B LEU* 3.3 26.0 - - + -
144B TYR* 1.3 80.0 - - - +
146B ILE* 1.3 65.2 + - - +
147B ALA 3.7 0.9 + - - -
157B ASP* 5.2 1.7 - - - +
173B LEU* 3.5 17.5 - - + -
175B ALA* 4.2 15.5 - - + -
229B VAL* 5.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 5.0 0.4 - - - -
144B TYR* 3.3 31.6 - - + +
145B PHE* 1.3 74.0 - - - +
147B ALA* 1.3 71.9 + - + +
148B PRO* 4.0 0.4 - - - +
152B GLY 5.3 2.9 - - - +
153B LEU* 4.8 14.8 - - + -
157B ASP* 3.9 22.0 - - + +
161B MET* 4.9 6.7 - - + -
172B PRO* 3.9 16.6 - - + +
173B LEU 3.0 22.9 + - - +
174B ILE* 4.1 16.5 - - + +
175B ALA* 3.1 27.5 + - - +
188B PHE* 4.9 10.3 - - + -
192B ILE* 5.3 10.3 - - + -
226B PRO* 6.4 0.2 - - + -
----------------------------------------------------------
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