Contacts of the helix formed by residues 250 - 258 (chain A) in PDB entry 1OWH
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 PHE 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS* 3.9 23.1 - + - -
108A ASN* 3.4 38.1 - - - -
110A ILE* 3.6 29.4 - - + -
193A LYS* 3.7 24.5 - - + -
245A THR* 3.5 27.1 - - + -
246A ARG 3.4 17.3 - - - -
247A VAL 3.0 7.6 + - - +
249A HIS* 1.3 97.2 - + - +
251A LEU* 1.3 57.7 + - - +
252A PRO* 3.4 3.6 - - - -
253A TRP* 3.1 12.0 + - + +
254A ILE* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.2 26.5 - - + -
135A PRO* 3.2 32.1 - - + +
136A SER* 3.8 2.7 - - - -
137A MET* 3.7 34.8 - - + +
247A VAL 3.6 6.0 + - - +
248A SER* 3.5 23.8 - - - +
249A HIS 3.4 0.4 - - - -
250A PHE* 1.3 74.4 - - - +
252A PRO* 1.4 62.9 - - + +
254A ILE* 3.4 9.1 + - + +
255A ARG* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 3.3 25.5 - - + -
249A HIS 3.4 14.1 - - - +
250A PHE 3.4 4.7 - - - -
251A LEU* 1.4 92.0 - - + +
253A TRP* 1.3 56.7 + - - +
255A ARG* 4.0 8.8 + - + +
256A SER* 2.9 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.1 0.2 - - + -
94A ILE* 4.1 16.8 - - + -
95A LEU 4.5 0.4 + - - -
96A HIS* 3.3 60.2 + + + +
97A LYS* 5.0 8.3 - - - +
110A ILE* 3.9 40.2 - - + -
111A ALA* 4.2 0.4 - - - -
112A LEU* 3.6 39.9 - - + -
250A PHE* 3.1 14.8 + - + +
252A PRO* 1.3 77.5 - - - +
254A ILE* 1.3 72.9 + - + +
256A SER* 3.5 3.9 + - - -
257A HIS* 2.9 66.1 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 5.1 2.5 - - + -
50A ILE* 3.6 31.0 - - + -
110A ILE* 4.2 6.7 - - + -
112A LEU* 4.5 6.3 - - + -
134A LEU* 4.2 26.2 - - + -
247A VAL* 4.0 23.8 - - + +
250A PHE* 2.8 29.4 + - + +
251A LEU* 3.9 8.5 - - + +
253A TRP* 1.3 90.7 - - + +
255A ARG* 1.3 60.1 + - - +
257A HIS 3.4 0.9 + - - -
258A THR* 2.8 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU 2.9 21.1 + - - +
252A PRO* 4.0 7.3 + - - +
254A ILE* 1.3 73.3 - - - +
256A SER* 1.3 79.0 + - - +
258A THR* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO 2.9 18.5 + - - -
253A TRP* 3.6 2.8 + - - -
255A ARG* 1.3 90.3 - - - +
257A HIS* 1.3 77.7 + - - +
258A THR 3.5 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.7 8.0 - - - -
94A ILE* 3.6 39.8 - - + +
95A LEU 6.0 0.7 - - - -
97A LYS* 4.7 12.9 + - - -
112A LEU* 3.8 17.2 - - + +
253A TRP* 2.9 64.0 + + - +
254A ILE 3.8 0.7 - - - -
255A ARG 3.3 0.2 - - - -
256A SER* 1.3 87.4 + - - +
258A THR* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.9 51.3 + - + -
112A LEU* 4.0 21.5 - - + -
254A ILE* 2.8 26.6 + - + +
255A ARG* 3.3 20.3 + - - +
256A SER 3.7 4.7 - - - +
257A HIS* 1.3 80.6 - - - +
----------------------------------------------------------
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