Contacts of the helix formed by residues 338 - 349 (chain F) in PDB entry 2AJQ
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 SER 338 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F ASN* 3.0 19.1 + - - -
336F PRO 3.0 0.4 - - - -
337F SER* 1.3 78.6 - - - +
339F ARG* 1.3 62.1 + - - +
340F ASP 3.4 4.0 + - - -
341F HIS* 2.9 28.4 + - - +
342F ILE* 2.9 27.8 + - - +
962Z T 3.4 19.8 + - - -
963Z G 2.7 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F SER 3.7 4.8 + - - +
338F SER* 1.3 70.7 - - - +
340F ASP* 1.3 57.7 + - - +
342F ILE* 3.3 11.1 + - - +
343F GLN* 2.9 32.2 + - - +
364F VAL* 2.7 49.7 + - + +
365F ASP* 4.1 7.9 - - - +
366F ASP* 4.7 0.4 - - - +
369F LEU* 4.5 3.4 - - - +
390F LEU* 3.5 43.8 - - - +
917X T 5.2 4.9 - - - +
918X G 3.5 43.2 + - - +
919X C 3.8 15.2 + - - -
962Z T 5.4 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 340 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLN* 4.7 10.4 + - - +
338F SER* 3.0 9.1 + - - +
339F ARG* 1.3 80.6 - - - +
341F HIS* 1.3 61.1 + - - +
343F GLN* 3.2 26.1 + - - +
344F LYS* 3.0 30.4 + - - +
962Z T 5.3 0.2 - - - +
963Z G 3.9 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 341 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F TRP* 3.9 18.2 - + + -
266F GLN* 4.1 15.8 + - - -
332F VAL* 4.0 23.9 - - + +
333F VAL 3.8 17.4 + - - -
334F PHE* 4.0 11.7 - - + -
335F ASN* 3.2 37.8 + - + +
338F SER* 2.9 25.5 + - - +
340F ASP* 1.3 79.5 - - - +
342F ILE* 1.3 63.1 + - - +
344F LYS* 3.4 5.1 + - + +
345F LYS* 3.1 29.1 + - - +
963Z G 3.6 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F PHE* 4.4 16.2 - - + -
336F PRO 3.3 26.0 - - - +
338F SER 2.9 21.2 + - - +
339F ARG* 3.6 16.4 - - - +
341F HIS* 1.3 76.7 - - - +
343F GLN* 1.3 59.2 + - - +
345F LYS* 3.5 1.7 + - - +
346F LEU* 2.9 53.9 + - + +
364F VAL* 3.9 20.0 - - + -
369F LEU* 4.1 8.3 - - + -
386F ILE* 3.6 31.9 - - + -
390F LEU* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 343 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F ARG 2.9 16.3 + - - +
340F ASP* 3.2 33.7 + - - +
342F ILE* 1.3 78.0 - - - +
344F LYS* 1.3 67.2 + - - +
347F GLN* 2.6 50.5 + - - +
351F TRP* 4.3 13.0 - - + -
361F ALA* 6.1 0.6 - - - +
362F PRO* 3.0 36.7 - - + +
364F VAL* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F TRP* 3.1 48.0 - - + +
265F TYR 4.6 2.9 + - - -
266F GLN* 4.0 19.5 + - - +
267F PRO* 5.3 4.2 - - - +
340F ASP* 3.0 19.9 + - - +
341F HIS* 3.8 5.6 - - + +
342F ILE 3.3 0.2 - - - -
343F GLN* 1.3 89.0 + - - +
345F LYS* 1.3 69.8 + - - +
347F GLN* 4.1 2.3 - - - +
348F GLU* 3.1 26.1 + - + +
31I TRP* 5.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 3.6 47.6 + - + +
264F TRP* 3.3 55.7 - - + +
334F PHE* 3.7 17.0 - - + -
341F HIS 3.1 16.2 + - - +
342F ILE* 4.0 2.2 - - - +
344F LYS* 1.3 89.6 - - - +
346F LEU* 1.3 65.0 + - + +
348F GLU* 3.5 33.8 + - - +
349F ALA* 3.2 21.5 + - - +
379F LYS* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 4.6 17.7 - - + -
342F ILE* 2.9 40.0 + - + +
345F LYS* 1.3 76.9 - - + +
347F GLN* 1.3 66.4 + - - +
349F ALA* 2.9 17.1 + - + +
350F GLY 3.3 0.5 + - - -
351F TRP* 3.1 39.2 + - + +
364F VAL* 5.4 0.2 - - + -
369F LEU* 4.1 16.6 - - + -
372F VAL* 3.9 25.1 - - + -
374F VAL* 4.3 7.5 - - + +
379F LYS* 5.0 3.8 - - + +
383F ILE* 4.1 25.4 - - + -
386F ILE* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 347 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F GLN* 2.6 48.8 + - - +
344F LYS* 4.1 2.2 - - - +
346F LEU* 1.3 76.6 - - - +
348F GLU* 1.3 58.2 + - - +
350F GLY* 2.8 19.8 + - - -
351F TRP* 3.3 34.6 + - + +
353F PRO* 3.5 24.1 - - - +
356F TYR* 4.9 3.6 + - - -
362F PRO* 4.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 5.9 0.2 - - - -
344F LYS* 3.1 20.0 + - + +
345F LYS* 3.5 36.7 + - - +
346F LEU 3.2 0.2 - - - -
347F GLN* 1.3 74.9 - - - +
349F ALA* 1.3 58.5 + - - +
350F GLY 3.3 1.0 + - - -
379F LYS* 4.7 14.3 + - - +
61I ASP* 5.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 6.0 0.2 - - + -
345F LYS 3.2 12.2 + - - +
346F LEU* 2.9 14.5 + - + +
348F GLU* 1.3 78.1 - - - +
350F GLY* 1.3 57.1 + - - +
374F VAL* 3.7 26.9 - - + +
375F ASP* 4.5 7.1 + - - +
376F ASP* 5.2 4.7 + - + +
379F LYS* 3.8 32.8 - - + +
----------------------------------------------------------
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