Contacts of the helix formed by residues 335 - 342 (chain A) in PDB entry 1XFV
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 ALA 335 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 5.4 0.2 - - + -
332A ASN* 3.5 13.5 - - - +
333A LYS 2.6 8.3 + - - -
334A LEU* 1.3 77.2 - - - +
336A THR* 1.3 56.2 + - - +
337A ASN 3.4 2.5 - - - -
338A LEU* 3.1 10.9 + - - +
339A ILE* 2.8 38.8 + - + +
362A GLY* 4.5 2.7 - - - +
489A THR* 3.1 25.6 - - + +
490A ALA* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLY* 2.8 31.0 + - - +
307A LEU 3.3 13.0 - - - +
308A VAL* 2.7 40.0 - - + +
309A PRO* 4.4 5.4 - - + -
331A VAL* 5.7 0.4 - - - -
332A ASN 3.6 3.0 + - - -
333A LYS* 2.8 25.2 + - - -
335A ALA* 1.3 75.4 - - - +
337A ASN* 1.3 68.4 - - - +
339A ILE* 3.2 7.2 - - - +
340A LYS 3.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS 4.6 8.7 + - - -
334A LEU* 5.8 0.4 - - - +
335A ALA 5.6 0.2 - - - -
336A THR* 1.3 74.4 - - - +
338A LEU* 1.3 58.0 + - + +
339A ILE 2.9 2.0 - - - -
340A LYS* 2.7 16.7 + - - +
341A SER* 2.3 41.2 + - - -
409A ARG* 4.3 7.6 - - - +
412A GLU* 2.4 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU 3.4 22.9 - - - +
335A ALA* 3.2 6.1 - - - +
337A ASN* 1.3 77.1 - - - +
339A ILE* 1.3 57.9 + - - +
341A SER* 3.0 10.8 - - - +
342A GLY 2.9 7.6 + - - -
343A VAL* 2.8 42.5 + - + +
362A GLY* 3.3 33.0 - - - +
363A TYR* 3.9 28.5 - - + +
409A ARG* 3.5 38.8 - - + +
489A THR* 3.8 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 3.9 0.7 - - + -
311A HIS* 3.6 24.9 - - + -
331A VAL* 4.4 9.0 - - + -
335A ALA* 2.8 25.2 + - + +
336A THR* 3.2 10.1 - - - +
337A ASN 2.8 0.6 + - - -
338A LEU* 1.3 71.9 - - - +
340A LYS* 1.3 58.9 + - - +
341A SER 2.9 0.9 - - - -
342A GLY* 2.7 22.3 + - - -
343A VAL 4.0 6.1 - - - -
345A THR* 4.4 5.8 - - + -
489A THR* 4.0 8.3 - - + -
490A ALA 3.4 25.6 - - - +
492A TYR* 3.6 33.0 - - + +
569A TYR* 3.0 26.9 - - + +
574A VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 3.7 26.2 - - + +
309A PRO* 5.7 8.3 - - - +
310A GLU* 2.9 33.9 + - + +
311A HIS* 4.6 6.5 - - + -
336A THR 3.1 3.5 + - - +
337A ASN* 2.7 19.5 + - - +
339A ILE* 1.3 76.9 - - - +
341A SER* 1.3 62.5 + - - +
342A GLY* 3.2 1.6 + - - -
568A GLY 5.5 2.8 - - - +
569A TYR* 5.1 5.0 - - - -
570A THR* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 2.3 33.8 + - - -
338A LEU* 3.0 21.3 + - - +
340A LYS* 1.3 69.5 - - - +
342A GLY* 1.3 55.1 + - - +
343A VAL* 4.4 6.9 - - - +
406A ASP* 4.9 13.9 + - - -
570A THR* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE 2.7 16.1 + - - -
340A LYS 3.2 2.0 - - - -
341A SER* 1.3 74.6 - - - +
343A VAL* 1.3 67.0 + - - +
344A ALA 3.4 0.7 + - - -
486A LYS* 3.8 16.3 + - - +
569A TYR* 4.4 8.3 - - - -
570A THR* 4.7 15.7 - - - -
571A GLY* 3.4 19.3 + - - -
----------------------------------------------------------
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