Contacts of the helix formed by residues 336 - 342 (chain J) in PDB entry 6XAV
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 336 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J MET 3.3 15.0 - - - -
331J ILE 3.8 19.3 - - - -
332J LYS 4.2 2.7 + - - -
333J GLY 3.4 8.8 + - - -
334J LYS 3.3 3.4 - - - -
335J GLN* 1.3 82.3 - - - +
337J ARG* 1.3 66.3 + - - -
338J PHE 3.2 3.1 - - - -
339J ARG 3.6 1.3 + - - -
340J GLN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254I VAL* 3.4 25.7 - - - +
1255I THR* 5.8 5.0 - - - -
1322I SER* 4.3 9.9 - - - +
1325I VAL* 3.9 12.8 - - - +
1326I LEU* 4.1 28.7 - - + -
1329I GLU* 3.3 25.3 + - - +
330J MET* 3.2 36.3 + - - +
331J ILE* 3.7 23.4 - - + +
335J GLN 4.6 7.3 + - - -
336J GLY* 1.3 72.5 - - - -
338J PHE* 1.3 57.0 + - - +
341J ASN* 2.9 37.6 + - - -
342J LEU* 2.8 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326I LEU* 3.5 33.9 - - + -
1330I ILE* 4.9 6.5 - - + -
331J ILE* 3.6 40.4 - - + +
336J GLY 3.2 0.8 - - - -
337J ARG* 1.3 76.8 - - - +
339J ARG* 1.3 59.5 + - + +
340J GLN 3.2 0.4 - - - -
342J LEU* 3.2 18.1 + - + -
343J LEU* 2.7 36.5 + - + +
1320J ILE* 4.0 19.1 - - + -
1323J ALA* 3.5 38.4 - - + +
1324J SER* 4.4 16.6 - - - -
1328J THR* 4.9 1.8 - - + -
1332J LEU* 5.9 2.9 - - + -
1352J ILE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269I ARG* 3.6 12.7 + - - -
1272I GLU* 4.9 3.6 + - - +
333J GLY 4.0 17.6 + - - +
334J LYS* 3.6 49.1 - - + +
336J GLY* 3.6 3.2 + - - -
338J PHE* 1.3 80.3 - - + +
340J GLN* 1.3 59.6 + - - +
343J LEU* 4.2 19.0 - - + +
344J GLY 5.0 2.7 + - - -
798J ARG* 3.7 40.4 - - - +
1323J ALA 5.7 0.4 - - - +
1324J SER 3.5 28.1 + - - +
1325J PHE* 5.6 2.2 - - - +
13T T 2.9 32.3 + - - -
15T T 4.4 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257I GLN* 4.4 2.6 - - - +
1269I ARG* 3.2 31.1 + - - +
334J LYS* 3.5 20.6 - - - +
335J GLN* 4.0 23.0 + - + +
336J GLY 3.1 15.9 + - - +
338J PHE 3.2 0.2 - - - -
339J ARG* 1.3 81.1 - - - +
341J ASN* 1.3 75.7 + - - +
344J GLY 2.8 19.2 - - - +
345J LYS* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255I THR* 4.1 15.2 - - - +
1257I GLN* 2.8 49.4 + - - +
1322I SER* 3.4 24.0 + - - +
335J GLN 5.2 0.5 - - - +
336J GLY 4.5 0.2 - - - +
337J ARG* 2.9 41.1 + - - +
340J GLN* 1.3 93.0 + - - +
342J LEU* 1.3 62.7 + - - +
344J GLY 4.2 1.1 - - - -
345J LYS* 3.4 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291I LEU* 5.2 1.7 - - - +
1320I PRO* 5.9 1.1 - - + -
1322I SER* 3.8 28.3 - - - +
1323I PHE* 4.2 5.2 - - + +
1326I LEU* 3.7 19.7 - - + -
337J ARG* 2.8 15.2 + - + +
338J PHE* 3.4 38.8 - - + +
340J GLN 3.9 0.2 - - - -
341J ASN* 1.3 85.9 - - - +
343J LEU* 1.3 65.3 + - + +
344J GLY 3.6 0.2 - - - -
345J LYS* 4.6 16.8 + - - +
1351J VAL* 4.3 19.6 - - - +
1352J ILE* 3.7 43.1 - - + +
----------------------------------------------------------
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