Contacts of the helix formed by residues 244 - 257 (chain A) in PDB entry 3AP3
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 HIS 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 3.0 37.4 + - - +
241A LEU 3.5 2.9 - - - -
243A LEU* 1.3 90.5 - - + +
245A PRO* 1.4 61.4 - - - +
246A ARG 3.2 3.3 + - - -
247A ARG* 3.4 16.5 + - + -
248A SER* 2.6 29.6 + - - +
335A GLY* 5.3 1.8 - - - -
336A ASN 3.2 30.6 + - - -
338A ASP* 3.6 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 3.0 28.4 - - + +
242A VAL 3.7 0.4 - - - +
243A LEU 3.2 13.9 - - - +
244A HIS* 1.4 85.1 - - - +
246A ARG* 1.3 57.8 + - - +
248A SER* 3.2 0.9 + - - -
249A LEU* 2.9 38.2 + - + +
265A LEU* 3.8 13.9 - - + -
293A VAL* 4.2 20.0 - - + -
338A ASP* 4.2 4.0 - - - +
340A PHE* 3.6 28.3 - - + -
341A VAL* 3.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A HIS 3.2 0.8 - - - -
245A PRO* 1.3 81.0 - - + +
247A ARG* 1.3 67.6 + - - +
250A LYS* 3.2 47.2 + - - +
260A TRP* 3.9 23.3 - - + +
262A ASP* 3.1 25.7 + - - +
265A LEU* 3.3 31.1 - - + +
338A ASP* 4.7 9.6 - - - +
340A PHE* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A HIS* 3.4 19.7 + - + +
246A ARG* 1.3 80.7 - - - +
248A SER* 1.3 67.1 + - - +
250A LYS* 3.2 24.9 - - - +
251A LEU* 3.3 47.4 + - + +
338A ASP* 5.1 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 6.2 0.9 - - - -
240A GLN* 3.2 21.0 + - - +
241A LEU* 3.4 23.0 - - - -
244A HIS* 2.6 24.6 + - - +
245A PRO 3.3 5.4 - - - -
247A ARG* 1.3 75.3 - - - +
249A LEU* 1.3 66.7 + - - +
251A LEU* 3.0 21.1 + - - +
252A ILE* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 3.9 18.6 - - + -
87A MET* 3.7 18.4 - - + -
88A LEU* 4.7 3.1 - - + -
241A LEU* 3.6 26.9 - - + -
245A PRO* 2.9 25.5 + - + +
246A ARG* 5.3 0.2 - - - -
248A SER* 1.3 72.2 - - - +
250A LYS* 1.3 65.7 + - - +
252A ILE* 2.8 23.6 + - + +
253A LEU* 2.8 39.7 + - + +
260A TRP* 4.4 5.8 - - + -
264A VAL* 3.1 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 3.2 49.7 + - - +
247A ARG* 3.2 19.5 + - - +
249A LEU* 1.3 81.8 - - - +
251A LEU* 1.3 66.7 + - + +
253A LEU* 3.4 2.8 + - - +
254A ASP* 3.0 21.2 + - - +
260A TRP* 3.5 35.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
234A LEU* 5.0 3.4 - - + -
247A ARG* 3.3 57.4 - - + +
248A SER* 3.0 9.5 + - - +
250A LYS* 1.3 81.2 - - + +
252A ILE* 1.3 53.1 + - + +
254A ASP* 3.0 9.9 + - + +
255A PHE* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 4.3 11.0 - - + -
88A LEU* 4.7 0.4 - - + -
179A LEU* 3.8 20.0 - - + -
234A LEU* 4.1 19.5 - - + -
236A VAL* 4.3 24.2 - - + -
241A LEU* 5.1 1.8 - - + -
248A SER* 3.0 27.5 + - - +
249A LEU* 2.8 39.4 + - + +
251A LEU* 1.3 77.5 - - + +
253A LEU* 1.3 55.6 + - + +
254A ASP 3.0 0.5 + - - -
255A PHE* 3.1 4.2 + - - +
256A LEU* 2.7 55.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.8 28.9 - - + -
91A HIS* 4.6 20.2 - - + -
94A VAL* 6.2 1.3 - - + -
249A LEU* 2.8 37.4 + - + +
250A LYS* 4.0 2.5 - - - +
252A ILE* 1.3 75.1 - - + +
254A ASP* 1.3 52.0 + - - +
256A LEU* 3.1 13.5 + - + -
257A GLY 2.5 30.8 + - - -
258A ILE* 3.0 35.5 + - + +
259A ALA 5.3 0.4 - - - +
260A TRP* 4.2 23.8 - - + -
261A SER 4.9 6.5 - - - +
264A VAL* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LYS 3.0 15.7 + - - +
251A LEU* 3.1 16.2 - - + +
252A ILE 3.0 0.2 - - - -
253A LEU* 1.3 74.2 - - - +
255A PHE* 1.3 67.8 + - - +
257A GLY* 2.9 16.0 + - - -
258A ILE 5.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 3.4 28.6 + - + -
178A PHE 3.8 2.0 - - - -
179A LEU* 3.3 30.7 - - + -
230A LYS 3.5 19.3 - - - -
231A GLU* 3.3 22.9 - - - -
232A LYS 3.1 27.6 - - - -
233A CYS 3.7 5.2 - - - -
234A LEU* 3.5 32.3 - - + -
251A LEU 2.7 15.0 + - - +
252A ILE 3.3 9.0 - - - +
254A ASP* 1.3 76.1 + - - +
256A LEU* 1.3 72.0 + - + +
257A GLY* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.3 26.2 - - + -
88A LEU* 4.2 11.2 - - + -
177A LYS* 4.1 29.3 + - + +
179A LEU* 3.8 15.9 - - + -
252A ILE* 2.7 44.4 + - + +
253A LEU* 3.2 27.8 - - + +
255A PHE* 1.3 93.7 - - + +
257A GLY* 1.3 59.5 + - - +
258A ILE* 4.4 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU 2.5 13.8 + - - -
254A ASP* 2.9 13.4 + - - -
255A PHE 3.3 0.4 - - - -
256A LEU* 1.3 77.9 - - - +
258A ILE* 1.3 60.2 - - - +
----------------------------------------------------------
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