Contacts of the strand formed by residues 20 - 26 (chain F) in PDB entry 1W4R
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 GLN 20 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ARG 4.6 5.5 + - - -
19F GLY* 1.3 76.4 - - - +
21F ILE* 1.3 61.2 + - - +
22F GLN* 3.0 35.5 + - + +
43F PHE* 5.4 4.0 - - - -
113F ALA* 3.8 6.8 - - - +
117F LYS 3.0 8.6 + - - +
118F THR* 3.8 25.4 + - + +
119F VAL* 2.8 33.1 + - - +
144F GLU* 3.3 29.6 - - + +
145F SER* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F GLN* 1.3 77.6 - - - +
22F GLN* 1.3 67.1 + - - +
23F VAL* 4.0 20.6 - - + -
109F CYS* 3.7 35.2 - - + +
110F GLU* 3.8 15.0 - - - +
113F ALA* 3.7 8.7 - - + -
119F VAL* 3.2 8.1 - - + +
121F VAL* 4.9 3.4 - - + -
139F LEU* 4.4 15.5 - - + -
142F LEU* 3.9 14.1 - - + +
143F ALA* 3.6 9.9 - - + +
144F GLU* 2.8 33.2 + - - +
145F SER 3.5 3.6 + - - -
186G ARG* 3.6 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F GLN* 3.0 36.9 + - + +
21F ILE* 1.3 75.1 - - - +
23F VAL* 1.3 63.6 + - - +
39F ARG* 3.0 40.7 + - - +
42F ARG* 5.8 1.9 + - - +
43F PHE* 5.1 6.5 - - - -
118F THR* 4.4 7.7 - - - +
119F VAL 2.8 11.3 + - - +
120F ILE* 3.4 19.6 - - + +
121F VAL* 2.8 28.1 + - - +
145F SER* 3.5 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ILE* 4.0 9.6 - - + -
22F GLN* 1.3 78.7 - - - +
24F ILE* 1.3 65.5 + - - +
25F LEU* 3.5 32.8 - - + -
39F ARG* 4.8 2.0 + - - -
121F VAL* 3.4 14.4 - - + +
123F ALA* 5.4 0.2 - - + -
136F ILE* 5.2 3.1 - - + +
139F LEU* 4.1 26.5 - - + -
140F VAL* 5.2 2.7 - - + +
143F ALA* 3.7 24.9 - - + -
145F SER* 2.9 8.3 + - - +
146F VAL* 3.3 11.9 - - + -
147F VAL* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 1.3 75.1 - - - +
25F LEU* 1.3 61.6 + - - +
32F LYS* 3.8 17.1 - - + +
35F GLU* 3.9 11.0 - - + -
36F LEU* 3.8 37.0 - - + +
39F ARG* 3.7 25.6 - - - +
120F ILE* 3.8 19.3 - - + -
121F VAL 2.7 12.8 + - - +
122F ALA* 3.4 3.2 - - - +
123F ALA 2.9 27.4 + - - +
147F VAL* 3.8 6.5 - - + -
149F LEU* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.5 25.8 - - + -
24F ILE* 1.3 76.5 - - - +
26F GLY* 1.3 54.2 + - - +
32F LYS* 3.7 4.1 - - - +
123F ALA* 3.2 22.4 - - + +
125F ASP* 4.0 20.6 - - + -
136F ILE* 4.3 8.3 - - + +
137F LEU* 4.1 10.3 - - + -
140F VAL* 4.5 6.3 - - + -
146F VAL* 4.0 20.2 - - + -
147F VAL 2.8 15.1 + - - +
148F LYS* 3.3 9.6 - - + -
149F LEU* 2.8 36.3 + - - +
140G VAL* 4.0 26.9 - - + -
146G VAL* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 1.3 79.3 - - - +
27F PRO* 1.3 75.6 - - - +
30F SER* 3.8 3.6 - - - -
32F LYS* 3.5 8.4 - - - +
123F ALA 3.5 0.8 + - - -
124F LEU* 3.3 19.9 - - - +
125F ASP* 3.2 18.4 + - - +
148F LYS* 4.0 4.0 - - - -
149F LEU 3.7 7.6 - - - -
----------------------------------------------------------
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