Contacts of the helix formed by residues 92 - 103 (chain A) in PDB entry 3ORH
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 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 2.8 28.3 + - - +
21A GLY 3.8 6.2 + - - -
23A ALA 2.6 28.1 + - - +
25A ALA* 3.4 8.6 - - - +
36A ILE* 4.0 15.3 - - - +
90A GLU* 3.0 14.1 + - - +
91A CYS* 1.3 76.0 - - - +
93A ASP* 1.4 52.3 + - - +
94A GLY* 2.9 10.9 + - - -
95A VAL* 2.9 31.6 + - + +
96A PHE* 2.8 34.8 + - - +
4000A SAH 3.6 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 2.9 28.2 + - - +
22A ALA* 4.2 8.2 - - - +
91A CYS 3.4 3.2 + - - +
92A ASN* 1.4 70.6 - - - +
94A GLY* 1.3 56.3 + - - +
96A PHE* 3.4 7.8 + - - +
97A GLN* 3.0 28.8 + - - +
114A LYS* 3.3 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 5.1 1.6 + - - -
24A PRO* 6.1 0.2 - - - -
25A ALA* 4.1 17.0 - - - -
92A ASN* 2.9 10.1 + - - +
93A ASP* 1.3 75.2 - - - +
95A VAL* 1.3 62.0 + - - +
97A GLN* 3.4 13.9 + - - +
98A ARG* 3.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 4.0 7.0 - - + -
27A TYR* 3.4 25.8 - - - +
34A LEU* 4.2 4.7 - - + -
36A ILE* 3.9 17.9 - - + -
69A PHE* 3.9 6.9 - - + -
70A GLY 3.6 14.4 - - - +
90A GLU* 3.5 20.9 - - + +
92A ASN* 2.9 26.3 + - + +
94A GLY* 1.3 73.0 - - - +
96A PHE* 1.4 60.4 + - - +
98A ARG* 3.0 5.8 + - - +
99A LEU* 2.9 24.4 + - - +
4000A SAH 3.5 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 3.8 12.9 - - + +
92A ASN 2.8 17.1 + - - +
93A ASP* 3.6 7.2 - - - +
95A VAL* 1.4 76.6 - - - +
97A GLN* 1.4 57.3 + - - +
99A LEU* 3.2 23.9 + - + +
100A ARG* 2.9 52.5 + - + +
112A PRO* 4.0 19.7 - - + -
113A LEU 3.5 30.1 - - - -
114A LYS* 3.5 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP 3.0 13.3 + - - +
94A GLY* 3.7 10.5 - - - +
95A VAL 3.2 0.6 - - - -
96A PHE* 1.4 76.7 - - - +
98A ARG* 1.4 60.8 + - + +
100A ARG* 2.9 41.8 + - - +
101A ASP* 2.9 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.4 66.9 + - + +
31A ASP* 4.4 11.3 + - - -
69A PHE* 4.0 10.3 - - + -
94A GLY 3.6 13.5 - - - +
95A VAL 3.0 8.6 + - - +
97A GLN* 1.4 76.9 - - + +
99A LEU* 1.4 55.5 + - - +
101A ASP* 3.4 10.3 + - - +
102A TRP* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.6 38.3 - - + -
88A ILE* 3.8 39.9 - - + +
90A GLU* 4.3 8.3 - - + -
95A VAL 2.9 11.8 + - - +
96A PHE* 3.2 27.8 + - + +
98A ARG* 1.4 76.0 - - - +
100A ARG* 1.3 57.6 + - - +
102A TRP* 3.2 6.8 + - + +
103A ALA* 2.9 34.3 + - - +
110A VAL* 4.2 10.5 - - + -
112A PRO* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 2.9 43.7 + - + +
97A GLN* 2.9 43.1 + - - +
99A LEU* 1.3 76.7 - - - +
101A ASP* 1.4 56.4 + - - +
103A ALA* 4.2 3.9 - - - +
104A PRO* 3.2 23.9 - - - +
112A PRO* 5.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 2.9 46.5 + - - +
98A ARG* 3.8 7.2 - - - +
99A LEU 3.3 0.2 - - - -
100A ARG* 1.4 75.3 - - - +
102A TRP* 1.4 60.5 + - - +
104A PRO* 3.4 10.9 - - - +
105A ARG* 3.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.6 22.4 - + + -
72A ALA* 4.1 12.2 - - + +
75A ALA* 3.8 35.4 - - + -
76A SER* 3.4 19.1 + - - -
79A GLN* 3.8 14.1 - - + -
86A HIS* 3.9 6.7 - - - -
88A ILE* 3.6 20.9 - - + -
98A ARG 3.0 17.2 + - - +
99A LEU* 3.2 6.5 + - + +
101A ASP* 1.4 77.0 - - - +
103A ALA* 1.3 77.1 + - - +
105A ARG* 3.3 36.1 - - - +
106A GLN* 2.7 61.6 + - + +
110A VAL* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 2.9 19.0 + - + +
100A ARG* 4.2 4.0 - - - +
102A TRP* 1.3 84.9 - - + +
104A PRO* 1.4 67.2 - - + +
106A GLN* 3.3 18.3 + - - +
110A VAL* 3.8 32.8 + - + +
112A PRO* 4.9 10.1 - - + -
----------------------------------------------------------
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