Contacts of the helix formed by residues 4 - 16 (chain A) in PDB entry 2ORY
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 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 5.0 2.9 - - - +
3A TYR* 1.3 78.6 - - - +
5A LYS* 1.3 64.3 + - - +
6A GLU* 3.5 17.3 + - - +
7A GLN* 2.7 44.7 + - - +
8A LEU* 2.9 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 1.3 73.6 - - - +
6A GLU* 1.3 63.9 + - - +
8A LEU* 3.1 11.5 + - + +
9A MET* 2.9 39.3 + - + +
167A LYS* 4.6 17.6 - - - +
169A CYS* 3.9 28.5 - - - +
202A SER* 4.3 11.9 + - - -
204A ILE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.2 16.5 + - - +
5A LYS* 1.3 87.8 + - - +
7A GLN* 1.3 58.9 + - + +
9A MET 3.4 1.1 + - - +
10A LEU* 3.0 23.2 + - - +
204A ILE* 4.0 22.2 - - + -
206A PHE* 3.3 12.1 - - - -
229A THR* 4.3 16.0 + - + +
231A ILE* 3.8 28.9 - - + -
320A MET* 5.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 3.9 4.2 - - - +
3A TYR* 3.4 15.0 - - + -
4A THR* 2.7 49.0 + - - +
6A GLU* 1.3 74.5 - - + +
8A LEU* 1.3 65.9 + - - +
10A LEU* 3.3 7.6 + - - +
11A ALA* 3.2 15.9 + - - +
320A MET* 3.1 34.0 + - + +
321A GLY* 4.5 4.4 + - - -
322A MET* 3.2 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 5.0 6.0 - - + +
4A THR 2.9 13.6 + - - +
5A LYS* 3.1 15.0 + - + +
7A GLN* 1.3 78.2 - - - +
9A MET* 1.3 63.2 + - - +
11A ALA* 3.0 25.6 + - - +
12A PHE* 3.1 27.3 + - + -
46A PRO* 3.7 29.8 - - + +
47A PHE* 4.1 11.7 - - + -
50A ASP* 5.8 0.9 - - - +
52A TRP* 3.8 30.5 - - + -
78A LYS* 5.8 1.8 - - - +
86A VAL* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 2.9 26.8 + - + +
6A GLU 3.9 4.0 - - - +
8A LEU* 1.3 77.2 - - - +
10A LEU* 1.3 59.7 + - - +
12A PHE* 3.7 8.7 - - - +
13A SER* 2.8 33.1 + - - -
86A VAL* 3.4 32.5 - - + -
169A CYS* 3.2 31.2 - - + +
171A THR* 3.2 46.5 + - + +
204A ILE* 3.8 22.0 - - + -
206A PHE* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 3.0 14.7 + - - +
7A GLN* 3.4 10.3 - - - +
9A MET* 1.3 75.6 - - - +
11A ALA* 1.3 58.2 + - - +
13A SER* 3.3 2.3 + - - -
14A TYR* 2.9 57.4 + - + +
206A PHE* 3.7 35.4 - - + -
316A TYR* 4.0 4.3 - - + -
317A PRO* 3.8 30.5 - - + -
320A MET* 4.0 19.5 - - + -
322A MET* 4.0 13.7 - - + -
326A ILE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN 3.2 8.6 + - - +
8A LEU 3.0 13.6 + - - +
10A LEU* 1.3 81.6 - - - +
12A PHE* 1.3 56.0 + - - +
14A TYR 3.5 0.2 + - - -
15A MET* 3.0 28.8 + - - +
44A TRP* 3.4 12.0 - - + -
46A PRO* 4.0 21.1 - - + -
47A PHE* 3.6 22.2 - - + -
322A MET* 4.3 3.6 - - + -
326A ILE* 3.9 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.1 46.9 + - + -
9A MET* 3.3 9.8 + - - +
11A ALA* 1.3 74.5 - - - +
13A SER* 1.3 63.3 + - - +
15A MET* 3.4 3.9 + - + -
16A SER* 2.8 15.6 + - - -
41A LEU* 3.9 12.8 - - + -
47A PHE* 3.5 24.0 - + - -
52A TRP* 3.8 30.5 - + - -
74A TYR* 2.8 25.9 + - - +
76A ILE* 3.7 31.2 - - + -
86A VAL* 3.9 29.4 - - + -
88A ALA* 4.5 2.5 - - + -
171A THR* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A MET 2.8 12.9 + - - -
10A LEU* 3.6 8.3 - - - -
12A PHE* 1.3 77.4 - - - +
14A TYR* 1.3 61.9 + - - +
16A SER* 3.1 24.7 - - - -
17A TYR* 3.8 11.3 - - - -
88A ALA* 5.0 0.4 - - - -
89A ILE 5.1 0.7 - - - +
171A THR* 3.0 28.7 + - - +
172A GLY* 3.1 19.4 + - - -
173A HIS* 4.0 23.3 + - - +
206A PHE* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 2.9 42.6 + - + +
11A ALA 4.1 2.9 - - - +
13A SER* 1.3 79.8 - - - +
15A MET* 1.3 62.9 + - - +
16A SER 3.0 2.0 - - - -
17A TYR* 3.0 24.1 + + - +
44A TRP* 4.7 0.2 - - + -
173A HIS* 3.3 42.1 + + + -
312A HIS 3.7 1.4 + - - -
313A VAL* 2.6 33.1 + - + -
316A TYR* 3.8 2.9 - - - +
317A PRO* 3.6 13.7 - - + +
326A ILE* 3.9 23.3 - - + -
328A LEU* 3.7 27.4 - - + -
331A ILE* 3.6 13.9 - - + +
332A PHE* 4.1 18.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.0 19.1 + - - +
12A PHE* 3.4 9.4 + - + +
14A TYR* 1.3 76.2 - - - +
16A SER* 1.3 61.6 + - - +
17A TYR 3.2 0.9 + - - -
18A TYR* 3.3 40.0 + - + +
37A MET* 3.9 35.1 - - + +
40A ALA* 3.7 16.6 - - + -
41A LEU* 4.1 18.6 - - + -
44A TRP* 3.8 12.5 - - + -
47A PHE* 3.7 22.9 - - - -
54A VAL* 5.3 0.4 - - + -
74A TYR* 3.4 37.2 - - + +
76A ILE* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE 2.8 22.2 + - - -
13A SER* 3.1 15.9 + - - -
15A MET* 1.3 78.6 - - - +
17A TYR* 1.3 57.8 + - - +
18A TYR 3.4 1.7 + - - +
72A MET* 3.4 22.7 - - - +
74A TYR* 3.4 17.8 + - - -
88A ALA* 3.7 7.8 - - - +
89A ILE 4.5 6.3 + - - -
90A ARG* 2.9 43.3 + - - -
----------------------------------------------------------
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