Contacts of the strand formed by residues 139 - 145 (chain F) in PDB entry 4XCS
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 LEU 139 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ALA* 3.6 18.8 - - + -
7F LYS 3.6 39.3 - - - +
8F ILE* 3.6 8.6 - - + +
9F GLY 2.9 29.1 + - - -
10F HIS 3.0 11.9 + - - +
12F ALA* 3.9 12.0 - - + +
13F PRO* 5.2 1.8 - - + -
116F TYR* 4.8 2.9 - - + -
131F PHE* 3.9 20.6 - - + -
132F ILE 3.7 9.0 - - - +
133F ILE* 4.1 11.9 - - + +
137F GLY 3.8 2.4 + - - -
138F ILE* 1.3 72.4 - - - +
140F ARG* 1.3 60.1 + - - +
141F GLN 3.7 18.2 - - - +
142F ILE* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ASN* 3.2 25.3 - - - +
146E ASP* 2.8 53.0 + - - +
147E LEU* 5.0 0.4 - - - +
148E PRO* 5.2 3.6 - - - +
8F ILE* 3.8 5.4 - - - +
38F TYR* 3.3 12.9 + - + +
132F ILE* 2.8 13.6 + - + +
133F ILE 4.5 0.4 - - - -
134F ASP* 3.2 40.7 + - + +
138F ILE* 3.4 22.2 - - - +
139F LEU* 1.3 78.6 - - - +
141F GLN* 1.3 60.5 + - - +
163F PHE* 3.5 32.9 - - + -
166F THR* 5.3 1.6 + - - -
167F ASP* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E THR* 3.8 7.9 - - + +
144E VAL 3.2 11.4 - - - +
145E ASN* 3.0 26.6 + - + -
8F ILE* 3.7 2.2 - - - +
130F LEU* 4.5 6.7 - - + +
131F PHE* 3.3 6.6 - - - -
132F ILE* 3.1 40.2 + - + +
139F LEU* 3.7 7.6 - - - +
140F ARG* 1.3 81.9 - - - +
142F ILE* 1.3 72.1 + - - +
143F THR* 3.0 22.1 + - - +
151F ARG* 5.2 2.0 - - - +
159F LEU* 3.5 38.1 - - - +
163F PHE* 3.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ILE* 3.6 1.8 - - + +
143E THR* 3.3 4.3 - - - +
144E VAL* 2.8 37.6 + - + +
1F MET* 3.6 50.5 - - + -
6F ALA* 4.2 11.0 - - + +
8F ILE* 3.8 15.0 - - + -
116F TYR 5.6 1.8 - - - +
130F LEU 3.6 3.1 - - - -
131F PHE* 3.9 23.3 - - + -
139F LEU* 3.9 22.9 - - + -
141F GLN* 1.3 78.0 - - - +
143F THR* 1.3 64.3 + - - +
144F VAL* 4.2 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLN* 4.0 18.2 - - - +
142E ILE 3.3 3.6 - - - +
143E THR* 2.8 24.9 + - - +
128F ARG 3.9 0.2 - - - +
129F GLY* 3.3 2.9 - - - -
130F LEU* 2.8 45.1 + - - -
141F GLN* 3.0 24.8 + - - +
142F ILE* 1.3 70.9 + - - +
144F VAL* 1.3 65.0 + - - +
145F ASN* 4.6 0.2 - - - +
151F ARG* 3.9 12.2 + - - +
201F GOL 3.7 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.4 21.1 - - + +
141E GLN* 3.3 1.9 - - - +
142E ILE* 3.0 52.6 + - + +
1F MET* 5.4 2.9 - - + -
117F GLY 5.6 0.7 - - - +
118F VAL* 3.7 30.1 - - + -
127F PHE* 3.9 11.4 - - + -
128F ARG 3.4 11.2 - - - +
129F GLY* 3.9 3.1 - - - -
131F PHE* 4.9 0.7 - - + -
142F ILE* 4.2 17.0 - - + -
143F THR* 1.3 80.8 - - - +
145F ASN* 1.3 63.4 + - - +
201F GOL 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 4.2 7.6 - - - +
140E ARG 3.1 17.7 - - - +
141E GLN* 2.9 31.4 + - + +
159E LEU* 5.0 0.2 - - - +
163E PHE* 4.1 2.2 - - + -
126F SER 3.7 1.0 - - - +
127F PHE* 3.2 3.4 - - - -
128F ARG* 3.2 28.5 + - - -
143F THR* 4.6 0.6 - - - +
144F VAL* 1.3 77.2 - - - +
146F ASP* 1.3 61.3 + - - +
147F LEU* 3.0 26.6 + - - +
201F GOL 2.8 42.7 + - - -
----------------------------------------------------------
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