Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 3WYR
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 PHE 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.7 7.5 - - - -
33A GLY* 1.3 81.5 - - - -
35A ASN* 1.3 55.5 + - - +
36A ILE* 2.7 23.8 + - + +
76A GLY* 3.9 1.0 - - - -
77A PHE* 2.9 46.7 + + + +
79A PRO* 3.7 36.6 - - + -
80A HIS* 6.2 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS 3.9 1.0 - - - +
29A HIS* 3.0 31.6 + - - -
30A TYR 2.9 38.2 + - - -
33A GLY 4.8 1.4 + - - -
34A PHE* 1.3 70.9 - - - +
36A ILE* 1.3 62.4 + - - +
37A PHE* 3.3 17.4 - - + -
56A TRP* 3.6 9.5 - - + +
57A ASN* 3.2 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 2.7 16.2 + - + -
35A ASN* 1.3 73.2 - - - +
37A PHE* 1.3 59.2 + - - +
54A ILE* 3.6 25.8 - - + -
55A PHE 3.7 2.2 - - - +
56A TRP* 3.6 38.1 - - + +
77A PHE* 2.9 43.3 + - + -
85A TRP* 3.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.7 5.2 - - + -
28A CYS* 3.1 61.9 - - + -
29A HIS* 3.5 2.2 - - - -
30A TYR* 3.6 21.5 - - + -
35A ASN* 3.3 43.1 - - + -
36A ILE* 1.3 73.2 - - - +
38A THR* 1.3 60.4 + - - +
54A ILE* 3.2 5.8 - - - -
55A PHE* 2.9 69.4 + + + -
57A ASN* 4.0 4.7 - - - -
74A CYS* 4.4 7.6 - - + -
75A ARG 3.3 3.1 - - - +
76A GLY* 3.6 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 1.3 72.9 - - - +
39A LEU* 1.3 67.6 + - - +
40A TYR* 4.0 2.3 + - + -
53A ARG 3.6 6.0 + - - -
54A ILE* 4.1 8.5 - - - +
73A ARG 3.6 0.5 - - - +
74A CYS* 3.3 23.1 - - - -
75A ARG* 3.1 34.1 + - + +
85A TRP* 3.8 13.4 - - + -
13B TRP* 3.4 39.4 - - + +
14B PRO* 4.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.6 27.6 - - + -
37A PHE 4.0 0.6 + - - -
38A THR* 1.3 78.0 + - - +
40A TYR* 1.3 73.5 + - - +
50A LEU* 3.8 40.1 - - + +
52A ASN* 5.4 1.7 + - - -
53A ARG* 2.8 41.2 + - + +
55A PHE* 4.1 16.8 - - + -
59A PHE* 5.2 1.3 - - + -
72A TYR* 3.7 30.5 - - + -
73A ARG 3.5 11.9 - - - +
74A CYS* 3.9 8.3 - - - -
92A LEU* 4.7 0.4 - - + -
14B PRO* 5.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.2 4.7 - - - -
39A LEU* 1.3 78.6 - - - +
41A LYS* 1.3 63.8 + - - +
42A LYS* 3.9 23.0 + - + +
46A PRO* 5.9 2.9 - - - -
50A LEU 5.8 0.7 - - - -
72A TYR* 3.4 6.1 - - - -
73A ARG* 2.9 66.7 + - + +
74A CYS 4.3 0.2 - - - -
75A ARG* 3.8 29.1 + - + -
88A PRO* 3.5 27.5 - - - +
14B PRO* 3.6 36.8 - - + -
15B SER* 3.8 23.0 - - - -
17B VAL 5.8 0.4 - - - -
23B HIS* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 1.3 78.1 - - - +
42A LYS* 1.3 60.3 + - - +
43A ASP* 2.8 39.7 + - - +
44A GLY* 3.3 34.0 + - - +
45A VAL 4.6 2.5 + - - +
46A PRO* 4.1 28.4 - - + +
67A ALA 4.4 8.7 + - - +
69A ALA 3.2 25.0 + - - -
70A GLY* 3.9 1.3 - - - -
71A THR 3.4 9.2 - - - +
72A TYR* 3.4 37.9 - - + +
19B PRO* 4.0 12.8 - - - +
----------------------------------------------------------
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