Contacts of the helix formed by residues 250 - 257 (chain A) in PDB entry 4D1Q
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 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP* 2.6 25.4 + - - -
249A ARG* 1.3 66.1 - - - +
251A ALA* 1.3 67.5 + - - -
252A ASN* 2.8 14.5 + - - -
253A VAL* 2.8 18.9 + - - +
254A VAL 2.8 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG 2.8 10.3 + - - -
250A GLY* 1.3 69.3 - - - -
252A ASN* 1.3 64.1 + - - +
254A VAL* 3.2 10.8 - - - +
255A LYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.0 18.6 - - - +
219A SER* 4.0 22.3 + - - +
220A THR* 5.2 0.4 - - - -
221A ALA* 4.0 12.3 - - - +
224A ILE* 4.0 14.1 - - + -
250A GLY* 3.2 15.8 - - - +
251A ALA* 1.3 72.6 + - - +
253A VAL* 1.3 70.8 + - - +
255A LYS* 3.1 8.1 + - - +
256A SER* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 3.6 30.5 - - + +
180A ASP* 5.3 1.8 - - - +
181A LEU* 3.6 34.8 - - + +
192A LEU* 6.3 0.4 - - + -
224A ILE* 4.2 4.5 - - + -
247A THR* 3.5 30.1 - - + +
248A ASP* 5.2 5.6 - - - +
250A GLY* 2.8 15.4 + - - +
252A ASN* 1.3 76.2 - - - +
254A VAL* 1.3 65.0 + - - +
256A SER* 2.8 27.3 + - - +
257A LEU* 2.9 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP 3.8 4.0 - - - +
249A ARG* 3.6 34.8 - - + +
250A GLY 2.8 11.3 + - - -
251A ALA* 3.2 20.4 - - - +
253A VAL* 1.3 73.3 - - - +
255A LYS* 1.3 67.0 + - + +
257A LEU 3.3 5.7 - - - +
258A ALA* 3.3 17.0 + - - +
262A ARG* 3.5 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 4.0 19.9 - - + +
222A GLU* 5.4 3.8 - - - +
251A ALA 3.1 14.0 + - - +
252A ASN* 3.5 4.9 - - - +
253A VAL 3.0 0.6 - - - -
254A VAL* 1.3 80.3 - - + +
256A SER* 1.3 68.8 + - - +
258A ALA* 2.7 30.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
179A ILE* 4.5 0.2 - - - +
221A ALA* 3.5 30.2 - - - +
224A ILE* 3.5 25.2 - - - +
225A TYR* 3.4 26.2 - - - +
228A LEU* 6.0 0.3 - - - +
252A ASN 2.8 11.6 + - - -
253A VAL* 2.8 18.5 + - - +
255A LYS* 1.3 71.5 - - - +
257A LEU* 1.3 74.1 + - - +
258A ALA 3.0 4.3 + - - -
259A ASN* 4.7 2.4 + - - -
260A ASN* 4.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 3.6 26.0 - - + -
225A TYR* 4.3 3.1 - - + -
228A LEU* 4.0 18.4 - - + -
245A PHE* 3.7 50.0 - - + -
247A THR* 4.7 2.0 - - + -
253A VAL* 2.9 8.4 + - + +
254A VAL 3.3 5.0 - - - +
256A SER* 1.3 91.3 + - - +
258A ALA* 1.3 63.2 + - - +
259A ASN 3.2 3.6 + - - -
260A ASN* 3.5 28.2 + - + +
262A ARG* 3.9 30.8 - - + +
----------------------------------------------------------
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