Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 2OQH
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 GLU 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.5 25.0 + - + -
38A VAL 3.2 7.6 - - - +
39A ARG* 2.4 43.1 + - + +
43A GLY 3.6 9.1 + - - +
44A VAL* 1.3 83.1 - - - +
46A GLY* 1.3 58.3 + - - +
47A TRP* 4.1 15.9 + - - +
107A ALA* 4.5 0.2 - - - -
110A LYS* 3.0 35.9 + - - +
359A GLU* 4.2 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.2 6.8 - - - +
38A VAL* 2.7 38.0 + - - -
45A GLU* 1.3 75.0 - - - +
47A TRP* 1.3 62.7 + - - -
103A ALA* 3.3 26.1 - - - +
106A ASP* 3.4 6.1 - - - -
107A ALA* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.5 17.7 - + - -
35A VAL* 3.7 21.1 - - + -
36A VAL 3.3 9.9 - - - -
37A ARG* 3.4 32.1 - - + +
45A GLU* 4.1 14.2 + - - +
46A GLY* 1.3 78.3 - - - -
48A GLY* 1.3 57.9 + - - +
103A ALA* 3.5 13.3 + - - -
106A ASP* 2.9 16.8 + - - +
110A LYS* 4.1 13.7 - - - +
304A ILE* 4.1 10.5 - - + -
353A LEU* 3.6 23.0 - - + +
355A VAL* 5.9 3.6 - - + -
357A VAL* 3.6 42.0 - - + +
359A GLU* 4.0 25.1 - - + -
362A LEU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.3 8.2 - - - +
36A VAL 2.8 34.7 + - - -
47A TRP* 1.3 76.0 - - - +
49A GLU* 1.3 61.5 + - - -
99A ALA* 3.7 24.9 - - - -
102A VAL* 4.1 8.1 - - - -
103A ALA* 3.9 1.2 - - - +
304A ILE* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 2.7 39.0 + - + +
34A THR 3.3 9.0 - - - +
35A VAL* 4.6 8.5 - - + -
48A GLY* 1.3 74.8 - - - +
50A THR* 1.3 64.8 + - - +
99A ALA* 4.6 3.3 - - - +
102A VAL* 5.0 1.8 - - - +
272A TYR* 3.1 27.5 + - - -
302A LEU* 2.9 42.6 + - - +
304A ILE* 3.4 28.1 + - + +
305A ALA* 3.2 25.0 + - - +
333A ASP* 5.2 0.9 - - - +
334A ILE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.1 22.4 + - - +
34A THR* 2.9 38.9 + - + -
49A GLU* 1.3 76.7 - - - +
51A MSE 1.3 66.3 + - - +
56A VAL* 3.6 24.5 - - + -
95A ALA* 2.8 39.5 + - - +
99A ALA* 3.7 17.9 - - + -
272A TYR* 3.7 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.6 22.1 - - - +
50A THR* 1.3 82.5 + - - +
52A TRP* 1.3 112.4 + - + +
56A VAL* 3.2 20.3 - - + +
91A TYR* 3.5 40.8 - - + +
92A LEU* 4.6 4.7 - - + -
95A ALA* 3.8 18.4 - - + -
272A TYR* 5.2 6.2 - - + +
299A GLY* 4.6 11.2 - - - +
88C PHE* 4.0 23.3 - - + -
----------------------------------------------------------
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