Contacts of the strand formed by residues 32 - 40 (chain H) in PDB entry 2A3W
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 ASN 32 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 4.0 9.4 - - - +
31H GLN* 1.3 102.3 + - - +
33H PHE* 1.3 67.5 + - - +
98H TRP 3.5 5.6 - - - -
99H GLU* 3.9 12.5 - - - +
100H SER 3.8 9.2 + - - -
101H SER* 5.0 0.9 + - - -
161H ASP* 3.3 22.1 + - - +
162H SER* 3.9 19.4 - - - +
163H VAL* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 4.2 13.7 - - + -
32H ASN* 1.3 76.2 - - - +
34H THR* 1.3 69.1 + - - +
35H LEU* 4.0 9.2 - - + -
61H LEU* 3.6 39.0 - - + -
73H LEU* 4.2 6.7 - - + -
75H ILE* 3.6 26.2 - - + -
96H VAL* 4.0 19.1 - - + -
97H SER* 3.2 4.4 - - - -
98H TRP* 3.1 59.9 + + + +
125H VAL* 4.6 4.0 - - + -
159H MET* 3.8 24.7 - - + -
160H TRP 3.1 15.3 - - - +
162H SER 3.2 10.0 + - - +
163H VAL* 4.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H PHE* 1.3 76.5 + - - +
35H LEU* 1.3 63.2 + - - +
36H CYS* 4.1 7.9 - - - -
96H VAL 3.4 10.5 - - - +
97H SER* 3.5 6.4 - - - -
159H MET* 3.1 6.2 - - - +
160H TRP* 2.8 45.7 + - + -
162H SER 2.7 20.9 + - - -
163H VAL* 3.4 1.9 - - - -
164H LEU* 3.0 29.5 + - + -
169H ILE* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H PHE* 4.0 7.2 - - + -
34H THR* 1.3 74.1 - - - +
36H CYS* 1.3 62.8 + - - +
37H PHE* 3.9 17.3 - - + -
50H PHE* 3.5 59.7 - - + -
61H LEU* 5.1 3.8 - - + -
63H VAL* 4.0 13.7 - - + -
94H ILE 3.8 0.7 - - - +
95H CYS* 3.2 2.4 - - - -
96H VAL* 2.8 47.2 + - + +
157H LEU* 3.9 13.9 - - + -
158H TYR 3.4 15.7 - - - +
159H MET* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H THR* 4.1 7.0 - - - -
35H LEU* 1.3 74.9 - - - +
37H PHE* 1.3 66.2 + - - +
93H HIS* 4.2 8.1 - - - +
94H ILE 3.1 4.3 - - - -
95H CYS* 2.0 47.3 - - - -
156H ASP 3.8 3.6 - - - +
157H LEU* 3.2 1.2 - - - +
158H TYR* 2.7 38.9 + - + +
160H TRP* 3.6 30.7 - - + -
164H LEU* 5.0 1.1 - - - -
169H ILE* 4.5 2.2 - - - -
172H ALA* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.9 30.3 - - + -
36H CYS* 1.3 80.9 - - - +
38H ARG* 1.3 68.7 + - - +
39H ALA* 4.4 3.6 - - + -
49H LEU* 3.5 46.0 - - + -
50H PHE* 4.7 3.8 - - + -
63H VAL* 4.3 8.5 - - + -
92H VAL 4.1 0.2 - - - +
93H HIS* 3.6 8.6 + - - -
94H ILE* 2.9 68.7 + - + +
96H VAL* 5.5 0.7 - - + -
154H ILE* 4.7 8.7 - - + -
155H GLY 3.7 7.9 - - - +
156H ASP 3.2 10.8 - - - -
157H LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 1.3 74.4 - - - +
39H ALA* 1.3 60.4 + - - +
92H VAL 3.3 11.4 - - - +
93H HIS* 3.7 25.0 - - + +
154H ILE* 3.2 7.8 - - - +
155H GLY* 2.8 39.8 + - - +
156H ASP* 2.8 32.1 + - + +
172H ALA 3.1 18.0 + - - -
173H TYR* 2.9 33.9 + - - -
174H GLN 4.4 0.2 - - - -
175H GLY* 3.8 12.3 - - - +
201H LEU* 4.8 2.2 - - - -
203H TRP* 3.6 18.8 - - + -
204H VAL* 3.6 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 4.3 8.9 + - + -
38H ARG* 1.3 74.8 - - - +
40H TYR* 1.3 60.9 + - - +
41H SER* 4.3 1.3 - - - -
47H TYR* 6.0 0.9 - - + +
49H LEU* 4.2 24.7 - - + -
90H ALA 4.2 0.3 - - - +
91H PRO* 3.5 1.6 - - - +
92H VAL* 2.8 53.4 + - + +
150H PHE* 4.3 8.3 - - + -
153H GLU 3.3 8.3 - - - +
154H ILE* 4.4 4.0 - - + -
203H TRP* 3.8 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H ALA* 1.3 75.8 - - - +
41H SER* 1.3 62.2 + - - +
89H PRO* 4.7 7.9 + - + +
90H ALA* 3.7 13.7 - - - -
91H PRO* 3.4 33.9 - - + +
152H GLY* 3.5 2.8 - - - -
153H GLU* 2.9 38.0 + - + +
203H TRP* 3.5 54.5 - + + +
83I LYS 5.1 2.6 + - - -
112I THR* 5.1 3.6 - - - +
113I PRO* 2.7 29.6 + - + -
114I LEU* 3.5 14.5 - - - +
115I VAL* 3.5 39.2 - - + +
----------------------------------------------------------
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