Contacts of the helix formed by residues 302 - 311 (chain J) in PDB entry 6K71
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 302 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ARG* 4.3 20.4 - - + +
56J PHE* 3.4 13.7 - - - -
196J CYS* 5.4 0.6 - - - -
198J GLU* 3.0 42.4 + - - +
300J VAL 4.3 0.3 - - - -
301J SER* 1.3 87.3 + - - +
303J LEU* 1.3 63.8 + - - +
304J HIS* 3.2 16.1 + - + +
305J MET* 3.3 22.5 + - - +
306J TYR 3.3 6.4 + - - -
428J ARG* 5.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J PHE* 3.4 25.4 - - + -
57J PHE 5.4 6.5 - - - +
59J ILE* 4.3 17.0 - - + -
68J LEU* 5.4 0.4 - - + -
302J ASN* 1.3 72.8 - - - +
304J HIS* 1.3 58.9 + - - +
305J MET 3.3 0.2 - - - -
306J TYR* 3.2 20.9 - - + +
307J SER* 2.9 26.9 + - - -
412J LEU* 3.7 31.4 - - + -
428J ARG* 3.4 26.8 + - - +
430J VAL* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 304 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J PRO* 3.8 23.8 + - + +
196J CYS* 3.3 44.6 - - + +
198J GLU* 4.6 1.1 + - - +
302J ASN* 3.1 18.9 + - - +
303J LEU* 1.3 76.3 - - - +
305J MET* 1.3 58.6 + - - +
307J SER* 3.3 8.7 + - - -
308J ALA* 3.0 25.9 + - + +
428J ARG* 3.4 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 305 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J PRO 4.0 7.4 - - - +
194J THR* 3.6 54.3 - - + +
196J CYS* 5.4 0.7 - - - -
198J GLU* 3.9 9.6 - - - +
298J ALA* 3.8 21.8 - - + -
299J ARG 3.7 14.1 - - - +
300J VAL* 3.7 21.5 - - + -
301J SER* 3.9 6.7 - - - +
302J ASN* 3.3 20.0 + - - +
304J HIS* 1.3 75.3 - - - +
306J TYR* 1.3 59.6 + - - +
308J ALA* 4.3 2.2 - - - +
309J VAL* 2.9 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J PHE* 5.0 0.2 - - + -
68J LEU* 3.6 36.1 - - + +
69J PRO 3.2 18.4 + - - -
70J LEU* 3.8 27.7 + - + +
75J LEU* 5.3 0.9 - - + -
300J VAL* 3.6 15.6 - - + +
302J ASN 3.3 3.4 + - - +
303J LEU* 3.1 26.8 + - + +
305J MET* 1.3 78.6 - - - +
307J SER* 1.3 56.9 + - - +
309J VAL* 4.3 0.8 - - - +
310J CYS* 3.0 36.1 + - + +
378J VAL* 5.9 0.3 - - - +
395J TYR* 3.4 34.2 - + - +
397J TRP* 3.1 28.3 + + - -
412J LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J LEU 2.9 11.7 + - - -
304J HIS* 3.5 12.6 - - - -
306J TYR* 1.3 77.9 - - - +
308J ALA* 1.3 57.3 + - - +
311J ALA* 3.0 30.9 + - - +
393J GLN* 5.0 7.3 + - - -
395J TYR* 3.2 26.3 + - - -
410J GLN* 5.0 5.0 + - - -
428J ARG* 5.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J PRO* 4.3 22.2 - - + +
194J THR* 4.2 23.6 - - + -
304J HIS* 3.0 17.3 + - + +
305J MET* 3.4 7.8 + - + +
307J SER* 1.3 76.4 - - - +
309J VAL* 1.3 58.3 + - - +
311J ALA* 3.4 5.2 + - - +
312J ASP* 3.0 36.7 + - - +
315J ARG* 5.1 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J LEU* 3.7 23.1 - - + -
156J ILE* 3.8 25.8 - - + -
194J THR* 5.6 2.9 - - + -
296J TYR* 5.9 6.1 - - + +
298J ALA* 4.9 14.4 - - + +
300J VAL* 4.9 10.1 - - + -
305J MET* 2.9 34.1 + - + +
306J TYR* 5.0 0.4 - - - -
308J ALA* 1.3 76.5 - - + +
310J CYS* 1.3 60.0 + - - +
312J ASP* 2.8 22.1 + - + +
313J VAL* 2.9 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 310 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J LEU* 3.6 45.1 - - + +
306J TYR* 3.0 22.4 + - + +
307J SER 3.8 0.2 - - - -
309J VAL* 1.3 76.4 - - - +
311J ALA* 1.3 57.4 + - - +
312J ASP 3.4 0.4 + - - -
313J VAL* 4.1 2.2 - - - +
314J ILE* 3.9 19.5 - - - +
376J ASN 5.8 1.1 - - - +
377J SER 5.6 0.2 - - - -
378J VAL* 3.6 29.7 - - - +
395J TYR* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J SER* 3.0 20.1 + - - +
308J ALA* 3.5 6.1 - - - +
310J CYS* 1.3 78.4 - - - +
312J ASP* 1.3 57.5 + - - +
313J VAL 3.8 0.2 - - - -
314J ILE* 4.6 1.3 - - - +
315J ARG* 3.0 41.2 + - - +
359J ASN* 5.7 3.7 - - - -
376J ASN* 5.3 19.3 - - + +
393J GLN* 6.5 0.4 - - - -
395J TYR* 4.7 4.3 - - - +
----------------------------------------------------------
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