Contacts of the helix formed by residues 294 - 305 (chain B) in PDB entry 1IAX
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 294 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 13.3 - - - +
233B HIS* 4.9 0.6 + - - -
267B LYS 3.7 0.6 + - - -
268B ASP* 3.1 54.0 + - - +
270B VAL 4.4 0.2 + - - -
271B HIS* 4.0 0.2 - - + -
292B SER* 3.2 10.1 - - - +
293B PHE* 1.3 76.9 - - - +
295B ASP* 1.3 58.2 + - - +
296B ASP* 2.8 27.8 + - - +
297B VAL* 2.9 23.2 + - + +
298B VAL* 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 2.5 31.3 + - - +
268B ASP* 4.9 1.9 + - - +
293B PHE 4.1 3.1 - - - +
294B ASN* 1.3 71.7 + - - +
296B ASP* 1.3 64.5 + - - +
298B VAL* 3.3 8.3 - - - +
299B ASN* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.6 20.7 - - + +
16A ALA 5.2 3.4 - - - +
268B ASP* 5.7 0.9 - - - +
294B ASN* 2.8 16.9 + - - +
295B ASP* 1.3 73.1 - - - +
297B VAL* 1.3 68.3 + - - +
299B ASN* 3.0 20.9 + - - +
300B CYS* 3.1 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.3 35.6 - - + +
16A ALA* 5.7 0.2 - - - -
134B ILE* 3.9 24.9 - - + -
137B CYS* 4.4 9.8 - - + +
138B LEU* 3.6 6.5 - - + -
271B HIS* 3.6 13.0 - - + +
290B ILE* 5.4 0.2 - - + -
292B SER* 3.2 28.0 - - - +
294B ASN* 2.9 18.0 + - - +
296B ASP* 1.3 73.7 - - - +
298B VAL* 1.3 66.9 + - - +
299B ASN 3.1 0.2 + - - -
300B CYS* 3.3 5.8 + - - +
301B ALA* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU 4.8 0.2 - - - +
120B ARG* 3.1 52.5 - - + +
122B VAL* 3.9 6.0 - - + +
290B ILE* 6.1 1.1 - - - -
292B SER* 3.6 19.1 - - - +
294B ASN 2.8 20.8 + - - +
295B ASP* 3.3 9.9 - - - +
297B VAL* 1.3 77.6 - - - +
299B ASN* 1.3 63.2 + - - +
301B ALA* 3.5 5.5 + - - +
302B ARG* 3.1 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 3.2 15.4 + - - +
296B ASP* 3.0 13.7 + - - +
298B VAL* 1.3 79.1 - - - +
300B CYS* 1.3 58.5 + - - +
302B ARG* 2.6 41.4 + - - +
303B LYS* 2.9 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.4 40.4 - - + +
19A GLU* 4.2 8.1 - - + +
161A TRP* 3.8 24.5 - - - -
137B CYS* 3.5 21.1 - - - -
296B ASP 3.1 9.2 + - - +
297B VAL* 3.9 4.3 - - - +
299B ASN* 1.3 77.6 - - - +
301B ALA* 1.3 57.7 + - - +
303B LYS* 3.3 8.3 + - - +
304B MET* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.7 11.1 - - + +
123B MET 4.6 0.3 - - - +
133B THR* 4.0 25.6 - - + +
134B ILE* 5.7 0.7 - - + -
137B CYS* 3.7 5.8 - - - -
290B ILE* 4.2 24.2 - - + +
297B VAL* 3.0 19.3 + - + +
298B VAL* 3.6 5.2 - - - +
300B CYS* 1.3 76.7 - - - +
302B ARG* 1.3 52.4 + - - +
304B MET* 3.4 2.4 + - - +
305B SER* 2.7 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.5 30.6 + - + +
93B HIS* 3.5 55.0 + - - +
99B ARG* 4.8 1.8 - - - +
119B GLU 2.8 24.5 + - - -
121B VAL 3.5 22.8 + - - -
122B VAL* 3.8 13.7 - - + +
298B VAL* 3.1 28.3 + - - +
299B ASN* 2.6 28.6 + - - +
301B ALA* 1.3 70.0 - - - +
303B LYS* 1.3 65.7 + - + +
305B SER* 2.6 24.9 + - - +
306B SER 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 2.9 47.5 + - - +
157A ARG* 3.7 10.4 + - - +
161A TRP* 3.7 15.1 - - + -
92B TYR* 4.5 10.0 - - + -
299B ASN* 2.9 23.0 + - + +
300B CYS* 3.6 7.6 - - - +
302B ARG* 1.3 76.9 - - + +
304B MET* 1.3 58.3 + - - +
306B SER* 2.8 24.8 + - - -
307B PHE* 4.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.9 18.4 - - + -
161A TRP* 3.6 26.9 - - + -
162A ARG* 3.6 35.2 + - + +
133B THR* 3.9 20.1 + - + -
136B PHE* 3.5 35.0 - - + -
137B CYS* 3.9 17.9 - - - -
300B CYS* 2.9 22.9 + - - +
301B ALA 3.7 4.0 - - - +
303B LYS* 1.3 71.6 - - - +
305B SER* 1.3 62.4 + - - +
306B SER 2.9 7.6 + - - -
307B PHE* 3.1 27.8 + - - +
308B GLY 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.5 18.7 + - - +
122B VAL* 3.9 7.4 - - - -
123B MET 3.1 30.5 - - - -
124B ALA* 5.4 1.1 - - - +
133B THR* 5.8 1.3 - - - -
301B ALA 2.7 13.9 + - - -
302B ARG* 2.6 20.9 + - - -
304B MET* 1.3 76.0 - - - +
306B SER* 1.3 57.2 + - - +
307B PHE 3.1 0.4 - - - -
308B GLY 3.1 5.0 + - - +
309B LEU* 3.0 38.1 + - - +
----------------------------------------------------------
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