Contacts of the strand formed by residues 140 - 144 (chain J) in PDB entry 3FFC
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 GLU 140 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J PRO* 3.7 3.5 + - + +
139J PRO* 1.3 75.3 - - - +
141J VAL* 1.3 60.3 + - - +
162J LEU 3.5 1.0 - - - +
163J ALA* 3.5 0.5 - - - -
164J THR* 2.7 51.2 + - - +
165J GLY* 5.6 0.9 - - - -
203J ARG* 4.9 10.4 + - - -
251J VAL* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J PRO* 4.1 6.3 - - + -
140J GLU* 1.3 79.7 - - - +
142J ALA* 1.3 60.2 + - - +
161J CYS* 4.6 7.6 - - - -
162J LEU 3.3 7.6 - - - +
163J ALA* 4.2 3.4 - - + -
226J CYS 4.1 5.2 - - - +
228J VAL* 3.4 34.1 - - + -
251J VAL* 3.7 26.3 - - + +
252J SER* 3.6 12.4 - - - +
253J ALA* 3.3 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I SER* 6.0 2.7 - - - +
139I SER 3.6 10.5 - - - +
140I SER* 3.3 27.6 - - - +
141J VAL* 1.3 76.0 - - - +
143J VAL* 1.3 64.3 + - - +
144J PHE* 3.6 19.5 - - + -
161J CYS* 3.6 3.5 - - - -
162J LEU* 2.9 32.7 + - + +
253J ALA* 3.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I SER* 3.4 29.6 + - - +
142J ALA* 1.3 75.0 - - - +
144J PHE* 1.3 77.0 + - - +
145J GLU 4.4 0.4 - - - +
159J LEU* 4.2 16.2 - - + -
160J VAL 3.6 4.5 - - - +
161J CYS* 4.6 0.2 - - - -
175J TRP* 4.4 8.5 - - + -
224J PHE 5.0 1.1 - - - +
226J CYS* 3.6 23.3 - - + +
253J ALA* 3.4 39.0 - - + +
254J GLU* 4.2 7.9 - - - +
255J ALA* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I LEU* 3.7 17.8 - - + +
135I ARG 3.4 10.3 - - - +
136I ASP* 3.6 40.4 - - + -
140I SER* 4.2 11.9 - - - -
142I LYS* 4.2 11.0 - - + -
144I VAL* 3.6 32.5 - - + -
142J ALA* 3.6 29.8 - - + -
143J VAL* 1.3 77.2 - - - +
145J GLU* 1.3 65.3 + - - +
159J LEU* 3.5 6.6 - - - +
160J VAL* 2.7 43.8 + - + +
162J LEU* 3.7 28.7 - - + -
----------------------------------------------------------
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