Contacts of the strand formed by residues 68 - 73 (chain A) in PDB entry 2W93
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 SER 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.2 8.5 - - - -
23A PHE* 4.8 1.3 - - - -
58A ALA* 2.7 44.4 + - - +
61A TYR* 3.7 17.7 - - - -
62A ALA* 3.5 5.9 - - - +
67A MET* 1.3 84.2 - - - +
69A CYS* 1.3 62.8 + - - +
94A GLY 3.1 3.2 + - - -
95A VAL* 3.5 9.7 - - - +
96A LEU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.3 0.4 - - - -
14A LEU* 3.9 33.9 - - + -
19A VAL* 4.1 11.8 - - + +
21A THR 4.8 1.0 + - - -
22A VAL* 3.7 9.7 - - + -
23A PHE* 3.0 28.4 + - - -
58A ALA* 4.5 3.6 - - - -
68A SER* 1.3 78.6 - - - +
70A ILE* 1.3 63.3 + - - +
71A ILE* 4.1 17.3 - - - -
96A LEU* 3.2 17.3 - - + +
98A VAL* 4.0 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.3 11.7 - - + +
24A GLY* 3.9 8.7 - - - -
51A GLU 4.0 3.6 - - - +
54A ALA* 3.8 9.9 - - + -
55A ALA* 3.6 36.3 - - + +
58A ALA* 4.1 9.2 - - + -
69A CYS* 1.3 75.0 - - - +
71A ILE* 1.3 64.9 + - - +
72A THR* 3.8 21.5 - - + -
81A ALA* 4.2 5.4 - - + -
85A ILE* 4.3 4.0 - - + -
95A VAL* 3.7 26.0 - - + -
96A LEU 2.9 4.9 + - - +
97A HIS* 3.4 15.9 - - + -
98A VAL* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.8 2.9 - - + -
11A PHE* 3.5 33.4 - - + -
22A VAL* 3.6 21.1 - - + -
23A PHE 2.8 8.3 + - - -
24A GLY* 3.1 22.2 - - - -
25A LEU 3.3 7.6 + - - +
30A ASN* 3.9 18.4 - - + +
33A LEU* 4.0 24.9 - - + -
34A LEU* 3.8 16.4 - - + -
45A TRP* 3.8 8.4 - - + -
69A CYS* 4.1 9.6 - - - -
70A ILE* 1.3 76.8 - - - +
72A THR* 1.3 66.4 + - - +
98A VAL* 3.1 16.6 - - + +
100A GLY 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY* 4.8 0.7 - - - -
25A LEU 4.1 3.8 - - - +
30A ASN* 3.1 13.6 + - - +
51A GLU* 3.9 21.8 - - + -
70A ILE* 3.8 20.2 - - + -
71A ILE* 1.3 78.9 - - - +
73A THR* 1.3 60.2 + - - +
77A GLY* 3.6 7.9 - - - +
78A GLU* 3.3 23.4 + - - +
81A ALA* 4.4 1.6 - - + -
97A HIS* 2.8 31.9 + - - +
98A VAL 2.9 5.3 + - - +
99A VAL* 3.5 3.7 - - - +
100A GLY 3.0 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 4.3 2.2 + - - +
26A PRO 4.7 0.9 - - - +
27A GLY* 3.9 21.6 - - - -
29A PHE* 3.6 26.2 + - - +
30A ASN* 3.6 7.1 - - - +
51A GLU* 5.1 0.4 + - - +
72A THR* 1.3 75.6 - - - +
74A PHE* 1.3 68.0 + - - +
76A VAL* 3.6 26.9 - - + -
77A GLY* 3.0 21.6 + - - +
78A GLU* 3.1 8.7 + - - +
99A VAL* 3.9 3.1 - - - -
100A GLY 4.0 2.2 - - - -
115A HIS* 4.2 5.7 - - + +
600B TPP 4.1 21.1 - - + -
----------------------------------------------------------
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