Contacts of the helix formed by residues 360 - 370 (chain B) in PDB entry 3U7U
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 ASP 360 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 5.4 1.2 - - - -
358B ALA 3.7 2.4 + - - -
359B ILE* 1.4 75.2 - - - +
361B PRO* 1.4 75.8 - - - +
362B GLU* 3.5 19.5 + - - +
363B LYS* 2.9 51.6 + - + +
364B LEU* 3.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 3.3 11.6 - - + +
360B ASP* 1.4 90.7 - - - +
362B GLU* 1.3 59.7 + - - +
364B LEU* 3.2 24.6 + - + +
365B ASN* 4.6 2.1 + - - -
383B PRO* 3.9 36.3 - - + -
385B ASN* 6.5 1.3 - - + -
386B MET* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ASP* 3.1 19.1 + - - +
361B PRO* 1.3 77.6 - - - +
363B LYS* 1.4 57.3 - - + +
365B ASN* 2.7 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 4.3 11.3 + - - +
328B ILE* 3.7 31.9 - - + +
329B ASP* 3.1 39.7 + - - +
359B ILE* 5.1 0.2 - - + -
360B ASP* 2.9 41.2 + - + +
362B GLU* 1.4 70.6 - - + +
364B LEU* 1.4 54.2 + - - +
365B ASN 3.0 10.5 + - - -
366B VAL* 3.2 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 4.0 12.3 - - + -
343B PHE* 3.8 31.0 - - + -
348B ILE* 4.3 4.7 - - + -
359B ILE* 4.5 11.4 - - + -
360B ASP 3.8 1.8 + - - +
361B PRO* 3.2 14.3 + - + +
362B GLU 3.1 1.0 - - - -
363B LYS* 1.4 75.6 - - - +
365B ASN* 1.3 58.9 + - - +
366B VAL 3.1 3.2 + - - -
367B PHE* 3.3 28.0 + - + -
382B TRP* 3.9 16.4 - - + -
383B PRO* 3.6 38.1 - - + -
386B MET* 3.9 11.2 - - + -
391B VAL* 3.4 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PRO 4.7 1.8 + - - -
362B GLU* 2.7 45.6 + - - +
363B LYS 3.0 1.6 - - - -
364B LEU* 1.3 74.2 - - - +
366B VAL* 1.4 62.3 + - - +
367B PHE 3.1 2.9 - - - -
368B ARG* 2.8 57.6 + - - +
369B THR* 6.1 0.2 - - - +
391B VAL* 3.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 3.8 30.5 - - + +
329B ASP* 4.7 3.6 - - - +
331B PHE* 3.9 25.7 - - + +
332B ILE* 3.6 34.8 - - + +
333B ASN 4.7 2.1 + - - +
334B CYS 5.0 0.2 - - - +
363B LYS* 3.2 20.6 + - + +
365B ASN* 1.4 77.6 - - - +
367B PHE* 1.3 69.5 - - + +
368B ARG 3.3 1.0 + - - -
369B THR* 3.1 24.4 + - - +
370B VAL* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 4.2 5.8 - - + -
328B ILE* 3.7 29.8 - - + -
331B PHE* 3.8 34.5 - + + -
341B LEU* 3.8 30.7 - - + -
343B PHE* 3.8 23.8 - + - -
364B LEU* 3.3 29.6 + - + +
365B ASN 3.1 0.8 - - - -
366B VAL* 1.3 77.4 - - + +
368B ARG* 1.3 55.6 + - - +
369B THR 3.1 5.4 - - - -
370B VAL* 3.0 39.9 + - + +
391B VAL* 3.1 13.7 - - + +
392B PHE* 3.7 28.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ASN* 2.8 45.7 + - - +
366B VAL 3.3 0.2 - - - -
367B PHE* 1.3 75.3 - - - +
369B THR* 1.3 59.2 + - + +
390B SER* 3.5 39.5 + - - +
391B VAL* 3.1 25.3 + - - +
393B SER* 4.6 9.9 + - - +
394B ASN* 3.3 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASN* 3.7 21.5 - - + +
334B CYS 2.7 32.1 + - - +
335B THR* 3.5 17.9 - - - +
365B ASN 6.1 0.2 - - - +
366B VAL 3.1 17.6 + - - +
368B ARG* 1.3 80.9 - - + +
370B VAL* 1.4 62.5 + - - +
371B ARG* 3.4 10.7 + - - +
394B ASN* 4.9 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PHE 5.7 0.2 - - - +
334B CYS* 3.1 19.0 + - + +
335B THR 3.7 3.1 - - - +
337B ILE* 3.9 25.4 - - + -
366B VAL 5.0 0.4 - - - +
367B PHE* 3.0 37.6 + - + +
369B THR* 1.4 77.0 - - - +
371B ARG* 1.3 60.4 + - - +
372B GLU 3.4 27.4 - - - +
373B ILE* 4.0 16.6 - - + -
392B PHE* 5.1 4.4 - - + -
394B ASN* 3.4 6.4 + - - +
395B LEU* 3.2 26.6 + - + +
----------------------------------------------------------
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