Contacts of the helix formed by residues 251 - 259 (chain A) in PDB entry 1UHG
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 GLY 251 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.8 17.0 - - - +
248A GLU* 2.8 27.0 + - - -
249A VAL 3.5 0.4 - - - -
250A SER* 1.3 77.3 - - - +
252A LEU* 1.3 66.4 + - - +
253A GLU 3.4 2.7 - - - -
254A GLN* 3.4 17.9 + - - +
255A LEU* 3.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.9 22.6 - - + +
249A VAL 5.0 2.4 + - - +
250A SER 3.5 1.6 - - - -
251A GLY* 1.3 77.4 - - - +
253A GLU* 1.3 65.7 + - - +
255A LEU* 2.9 10.3 + - + +
256A GLU* 2.9 46.3 + - + +
363A PRO* 3.6 38.4 - - + +
364A PHE* 4.2 4.7 - - - +
365A LEU* 3.9 26.2 - - + -
381A ARG* 3.7 22.4 - - + +
383A VAL* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 5.2 6.0 + - - +
250A SER 4.8 5.7 + - - +
251A GLY 3.4 0.8 - - - -
252A LEU* 1.3 78.5 - - - +
254A GLN* 1.3 64.0 + - - +
256A GLU* 3.4 11.1 + - - +
257A SER* 3.1 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 5.1 2.2 + - - +
251A GLY* 3.4 12.7 + - - +
252A LEU 3.2 0.4 - - - -
253A GLU* 1.3 79.9 + - - +
255A LEU* 1.3 63.7 + - - +
257A SER* 2.4 28.7 + - - +
258A ILE* 3.1 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MET* 3.8 40.4 - - + -
244A LEU* 4.0 15.3 - - + +
246A PRO* 4.1 20.9 - - + -
251A GLY 3.5 7.9 + - - +
252A LEU* 2.9 10.6 + - + +
254A GLN* 1.3 79.2 - - - +
256A GLU* 1.3 58.8 + - - +
258A ILE* 3.1 13.2 + - + +
259A ILE* 3.0 33.0 + - + +
267A TRP* 3.9 23.1 - - + -
365A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.6 24.0 - - + -
19A LYS* 2.9 38.6 + - - +
252A LEU* 2.9 37.7 + - + +
253A GLU* 3.7 7.5 - - - +
255A LEU* 1.3 75.0 - - - +
257A SER* 1.3 62.4 + - - +
259A ILE* 4.0 18.1 - - - +
365A LEU* 3.6 18.9 - - + +
381A ARG* 2.8 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 5.7 2.5 - - - +
253A GLU* 3.1 11.1 + - - -
254A GLN* 2.4 36.6 + - - -
256A GLU* 1.3 81.4 - - - +
258A ILE* 1.3 62.4 + - - +
259A ILE 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 3.2 33.7 - - + +
227A MET* 5.3 0.2 - - - -
254A GLN* 3.1 31.8 + - - +
255A LEU* 3.1 23.1 - - + +
257A SER* 1.3 82.6 - - - +
259A ILE* 1.3 63.1 + - - +
260A ASN* 3.6 7.3 + - - -
263A LYS* 3.5 25.1 - - + +
267A TRP* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.7 41.8 - - + +
15A PHE* 4.9 6.7 - - + -
244A LEU* 3.7 29.8 - - + -
255A LEU* 3.0 22.8 + - + +
256A GLU* 4.0 17.0 - - - +
257A SER 3.6 4.3 - - - +
258A ILE* 1.3 79.3 - - - +
260A ASN* 1.3 71.5 + - - +
263A LYS* 4.5 0.4 - - - -
264A LEU* 4.4 9.0 - - + -
267A TRP* 4.1 15.0 - - + -
365A LEU* 4.5 16.2 - - + -
379A PHE* 4.7 5.6 - - + -
----------------------------------------------------------
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