Contacts of the strand formed by residues 37 - 46 (chain A) in PDB entry 1WWL
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 ASP 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.1 27.3 + - - +
14A SER* 4.1 12.6 - - - -
15A CYS* 3.1 23.3 + - - +
35A ALA 4.2 0.7 - - - +
36A ALA* 1.3 93.9 - - - +
38A VAL* 1.3 66.3 + - - +
73A LYS* 5.1 0.2 - - - +
74A ARG* 2.6 55.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 3.9 13.2 - - + +
17A CYS* 4.5 0.2 - - + -
32A CYS* 3.8 29.4 - - + +
35A ALA 3.8 15.7 - - - +
37A ASP* 1.3 81.0 - - - +
39A GLU* 1.3 65.1 + - - +
40A LEU* 3.7 26.2 - - + -
72A LEU* 3.9 12.8 - - + -
74A ARG 3.1 7.4 + - - +
75A LEU* 3.6 17.8 - - + +
76A THR* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 6.4 1.8 - - - -
15A CYS 3.5 5.4 + - - +
16A SER* 3.1 29.6 + - - +
17A CYS* 2.8 26.3 + - - +
38A VAL* 1.3 76.5 - - - +
40A LEU* 1.3 65.0 + - - +
41A TYR* 4.0 3.6 + - + +
76A THR* 3.7 12.3 - - - +
78A ARG* 2.6 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 3.4 21.3 - - + +
19A PHE* 4.0 23.8 - - + -
38A VAL* 3.7 24.2 - - + -
39A GLU* 1.3 73.6 - - - +
41A TYR* 1.3 61.4 + - - +
42A GLY 3.8 0.9 - - - +
75A LEU* 4.5 9.4 - - + -
76A THR 3.0 13.6 + - - +
77A VAL* 3.9 29.3 - - + +
78A ARG* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 6.0 1.6 - - - +
17A CYS 3.5 11.0 + - - +
18A ASN* 3.7 14.9 - - + +
19A PHE* 3.4 20.4 + - - +
20A SER* 3.6 14.8 + - - -
39A GLU* 4.0 4.6 + - + +
40A LEU* 1.3 73.3 - - - +
42A GLY* 1.3 60.2 + - - +
43A GLY* 3.2 26.3 + - - -
78A ARG* 3.5 22.4 - - + -
79A ALA* 3.3 26.3 - - + +
2D NAG 4.9 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.2 10.8 - - - -
20A SER* 3.9 7.1 - - - -
40A LEU* 3.8 2.0 + - - +
41A TYR* 1.3 71.6 - - - +
43A GLY* 1.3 56.1 + - - +
45A ARG* 2.8 34.2 + - - +
47A LEU* 6.1 2.0 - - - -
78A ARG 2.7 12.1 + - - -
79A ALA 2.7 14.8 - - - -
80A ALA* 4.0 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.3 9.7 - - - +
41A TYR* 3.0 41.1 + - - -
42A GLY* 1.3 77.1 - - - +
44A GLY* 1.3 57.0 + - - -
45A ARG* 3.1 2.3 + - - +
79A ALA* 2.7 8.1 + - - +
2D NAG 4.2 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 1.3 70.8 - - - -
45A ARG* 1.3 63.9 + - - +
46A SER* 3.6 2.3 + - - -
79A ALA* 2.7 27.1 + - - +
80A ALA* 3.9 4.3 - - - -
81A ARG* 4.3 7.3 + - - +
2D NAG 3.9 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.8 35.6 + - - +
20A SER 3.1 18.8 - - - +
21A ASP 3.2 8.8 + - - -
22A PRO* 3.2 21.4 + - - -
24A PRO* 3.4 17.2 - - - +
26A TRP* 3.9 9.5 - - - -
42A GLY* 2.8 18.4 + - - +
43A GLY 3.1 3.0 + - - -
44A GLY* 1.3 76.5 - - - +
46A SER* 1.3 67.1 + - - +
47A LEU* 3.4 29.3 + - + +
49A TYR* 2.6 39.5 + - + -
80A ALA* 3.5 5.7 - - - +
81A ARG 3.2 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.6 2.0 + - - -
45A ARG* 1.3 81.7 - - - +
47A LEU* 1.3 66.7 + - - +
48A GLU* 3.3 21.8 + - - +
49A TYR* 3.6 17.6 - - - -
81A ARG* 3.3 41.2 + - - -
----------------------------------------------------------
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