Contacts of the strand formed by residues 141 - 145 (chain B) in PDB entry 4ZZ7
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 VAL 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.2 9.4 - - + +
49B ALA* 3.6 22.4 - - + +
50B GLN* 3.5 51.7 + - + +
53B PHE* 5.3 0.4 - - + -
140B GLY* 1.3 71.4 - - - -
142B VAL* 1.3 64.0 + - - +
168B CYS* 3.5 4.9 - - + +
170B VAL* 4.0 18.2 - - + -
216B ARG 3.4 15.5 + - - +
217B VAL* 3.5 15.9 - - + -
218B LYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 4.3 11.4 - - + -
140B GLY 3.9 1.3 - - - +
141B VAL* 1.3 81.2 - - - +
143B ALA* 1.3 67.7 + - - +
162B ALA* 4.7 0.4 - - + -
167B ASN* 3.8 32.5 - - + +
168B CYS 2.8 11.1 + - - +
169B PHE* 3.3 20.9 - - + -
170B VAL* 2.8 26.3 + - - +
217B VAL* 4.8 0.4 - - - -
219B ALA* 3.7 22.0 - - + +
221B SER* 5.4 0.4 - - - +
471B TYR* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 1.3 80.6 - - - +
144B GLY* 1.3 59.3 + - - +
145B ILE* 5.6 1.1 - - + -
169B PHE* 4.2 0.7 - - - -
170B VAL 3.3 6.5 - - - +
211B LEU* 4.2 29.4 - - + -
217B VAL* 3.7 23.0 - - + +
219B ALA 3.0 10.5 + - - +
220B VAL* 3.5 13.8 - - + -
221B SER* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 1.3 73.6 - - - +
145B ILE* 1.3 61.8 + - - +
158B MET* 3.7 7.9 - - - -
169B PHE* 3.5 22.8 - - - -
170B VAL 2.8 12.0 + - - +
171B LEU* 3.4 7.8 - - - +
172B LYS* 2.7 32.6 + - - +
211B LEU* 5.1 0.2 - - - +
221B SER 3.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 5.4 0.9 - - + -
144B GLY* 1.3 80.4 - - - +
146B THR* 1.3 66.3 + - - +
158B MET* 3.7 4.0 - - - +
172B LYS* 3.4 25.6 - - + +
208B VAL* 3.8 41.7 - - + +
211B LEU* 4.7 10.1 - - + -
212B LEU* 4.9 3.1 - - + -
220B VAL* 4.2 22.0 - - + -
221B SER 3.0 9.6 + - - +
222B PHE* 3.4 27.2 - - + -
223B VAL 3.0 26.0 + - - +
232B ILE* 4.3 8.3 - - + -
----------------------------------------------------------
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