Contacts of the strand formed by residues 35 - 39 (chain Y) in PDB entry 2AW2
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 THR 35 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124X ILE* 3.4 2.6 - - - -
125X GLU* 2.7 43.7 + - - +
9Y TYR* 4.4 6.4 - - - +
16Y CYS* 4.0 4.0 - - - +
17Y PRO* 2.8 42.8 + - - +
19Y CYS* 4.1 6.3 - - - -
25Y VAL* 4.2 11.2 - - + -
27Y GLU 3.8 10.8 - - - +
29Y CYS* 4.0 16.2 - - - +
34Y GLY* 1.3 70.7 - - - -
36Y VAL* 1.3 69.9 + - - +
37Y CYS* 3.8 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X ASP* 6.1 0.7 - - - +
36X VAL 5.3 1.3 - - - +
37X GLN* 3.6 26.7 - - - +
119X PHE* 5.4 3.6 - - + -
122X ASN* 4.5 14.1 - - + +
123X LEU 3.6 6.1 - - - +
124X ILE* 4.2 16.4 - - + -
25Y VAL* 3.9 0.3 - - - -
26Y LYS* 3.1 34.3 + - + +
27Y GLU* 3.2 41.4 + - + +
28Y ALA 6.0 0.4 - - - +
34Y GLY 3.5 1.8 + - - +
35Y THR* 1.3 76.9 - - - +
37Y CYS* 1.3 70.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 37 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122X ASN* 3.5 9.7 - - - +
123X LEU* 2.5 42.6 + - + +
125X GLU* 3.9 20.2 - - - -
19Y CYS* 2.0 56.5 - - + -
20Y SER 4.6 0.4 - - - -
23Y TYR* 3.9 9.6 - - + -
24Y ARG 3.3 5.4 - - - -
26Y LYS* 4.7 0.2 - - - -
35Y THR* 4.1 6.5 - - - -
36Y VAL* 1.3 79.2 - - - +
38Y GLU* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122X ASN* 4.2 10.2 + - - +
23Y TYR* 3.7 4.4 - - - -
24Y ARG* 2.7 76.4 + - - +
25Y VAL 4.9 0.2 - - - +
26Y LYS* 3.5 40.4 - - + +
37Y CYS* 1.3 79.7 - - - +
39Y PRO* 1.3 80.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121X SER* 3.6 37.9 - - - +
122X ASN* 3.9 11.9 - - - +
22Y GLY 3.4 9.9 - - - +
23Y TYR* 3.5 13.9 - - + +
24Y ARG* 4.9 2.3 + - - -
38Y GLU* 1.3 96.8 - - + +
40Y CYS* 1.3 67.7 + - - +
41Y PRO* 3.6 6.1 - - - +
75Y ARG* 4.1 22.9 - - - +
----------------------------------------------------------
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