Contacts of the strand formed by residues 23 - 28 (chain B) in PDB entry 5WFE
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 GLY 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN 3.6 0.8 + - - -
22B TYR* 1.3 76.1 - - - +
24B GLN* 1.3 63.9 + - - -
25B ILE 3.8 0.2 + - - -
34B LEU* 3.6 17.1 - - - +
35B ILE 3.6 11.4 - - - -
36B ASP* 4.4 7.6 - - - -
37B LYS 5.2 1.6 - - - -
57B GLY 3.0 10.5 + - - -
58B THR* 3.2 23.3 - - - +
59B ARG* 3.5 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.5 18.8 + - - -
23B GLY* 1.3 71.5 - - - -
25B ILE* 1.3 61.4 + - - +
26B ASP* 3.7 19.1 + - - +
34B LEU* 3.4 2.8 - - - +
35B ILE* 2.9 56.5 + - + +
36B ASP 5.3 3.4 + - - +
37B LYS* 6.3 0.2 - - - +
59B ARG* 2.6 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.8 0.2 + - - -
20B LEU* 4.0 26.0 - - + -
23B GLY 4.3 5.2 - - - +
24B GLN* 1.3 70.3 - - - +
26B ASP* 1.3 72.9 + - - +
32B PHE* 3.5 37.0 - - + -
33B VAL 4.4 1.3 - - - +
34B LEU* 3.6 26.7 - - + -
54B LEU* 4.5 5.8 - - + -
58B THR* 4.4 6.7 - - + -
59B ARG 2.5 19.0 + - - +
60B VAL* 3.6 28.0 - - + -
61B SER* 3.2 18.2 + - - -
64B ALA* 3.6 13.0 - - + -
75B LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.7 48.4 + - - -
24B GLN* 3.7 19.7 + - - +
25B ILE* 1.3 85.0 - - - +
27B VAL* 1.3 69.5 + - - +
28B ILE* 5.4 2.0 - - + -
32B PHE* 4.2 1.4 - - - -
33B VAL* 2.8 31.8 + - - +
35B ILE* 3.8 17.2 - - + +
61B SER* 3.4 4.2 - - - -
64B ALA* 4.7 1.1 - - - -
3G A 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 1.3 77.2 - - - +
28B ILE* 1.3 67.6 + - - +
30B GLY* 3.7 6.1 - - - +
31B ALA 3.2 27.4 - - - +
32B PHE* 4.7 3.4 - - + -
63B ALA* 4.0 10.8 - - + +
64B ALA* 3.6 33.9 - - + +
67B LEU* 4.0 17.3 - - + -
3G A 2.8 32.0 + - - +
4G C 3.4 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.3 2.2 - - + -
27B VAL* 1.3 77.1 - - - +
29B ASP* 1.3 88.1 + - + +
30B GLY 3.1 1.1 - - - -
31B ALA* 3.0 24.9 + - - +
33B VAL* 4.7 16.5 - - + +
35B ILE* 4.6 15.7 - - + -
41B ARG* 3.7 31.0 - - - +
43B HIS* 6.4 1.8 - - + -
17F GLY* 4.3 0.5 - - - -
3G A 5.8 0.2 - - - +
4G C 3.5 2.0 - - - -
----------------------------------------------------------
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