Contacts of the helix formed by residues 379 - 384 (chain B) in PDB entry 7V3X
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 379 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 6.1 0.9 - - - -
317B TYR* 4.4 4.2 - - - +
318B GLU* 2.7 31.7 + - - +
377B ILE* 3.7 3.8 - - - -
378B ASP* 1.3 75.0 + - - +
380B LEU* 1.3 62.8 + - - +
381B SER* 3.4 8.2 + - - -
382B ALA* 3.3 25.0 + - - +
383B LEU* 3.6 14.3 + - - +
413B THR* 3.0 27.6 - - - -
414B ASN* 4.5 1.3 - - - -
415B THR* 4.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 4.4 6.5 - - + -
377B ILE* 4.3 5.6 + - + -
379B SER* 1.3 67.9 - - - +
381B SER* 1.3 58.6 + - - +
382B ALA 3.1 1.8 - - - -
383B LEU* 3.0 23.8 + - + +
384B ALA 3.0 10.0 + - - -
392B PHE* 3.4 20.4 - - + -
395B PHE* 4.5 16.8 - - + -
396B VAL* 4.3 26.7 - - + -
399B VAL* 6.2 1.3 - - + -
412B PHE* 3.5 48.5 - - + -
413B THR 2.8 14.1 + - - +
414B ASN* 5.0 5.6 - - + +
430B ILE* 3.9 25.6 - - + -
434B THR* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 4.5 1.4 + - - -
379B SER* 3.4 7.8 + - - -
380B LEU* 1.3 76.7 - - - +
382B ALA* 1.3 63.2 + - - +
384B ALA* 3.4 10.0 + - - +
385B ARG* 3.4 21.0 + - - +
392B PHE* 5.2 0.9 - - - -
413B THR 4.2 1.4 + - - -
414B ASN* 3.6 17.4 + - - -
415B THR* 3.3 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TYR* 4.2 3.6 - - + -
318B GLU* 3.7 18.8 - - + +
351B PRO* 3.4 18.2 - - + +
379B SER* 3.3 24.1 + - - +
380B LEU 3.1 0.4 - - - -
381B SER* 1.3 82.0 + - - +
383B LEU* 1.3 56.3 + - - +
385B ARG* 3.1 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TYR* 3.7 48.0 - - + -
351B PRO* 4.0 18.2 - - + +
356B LEU* 3.8 22.6 - - + +
359B HIS* 4.3 16.6 - - + +
363B ILE* 5.2 0.9 - - + -
377B ILE* 5.7 3.6 - - + -
379B SER 3.9 12.1 - - - +
380B LEU* 3.0 17.1 + - + +
382B ALA* 1.3 72.1 - - - +
384B ALA* 1.3 60.1 + - - +
385B ARG 3.2 12.0 + - - +
387B VAL* 4.2 3.5 - - - +
392B PHE* 4.5 9.1 - - + -
395B PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU 3.0 7.7 + - - +
381B SER* 3.8 9.9 - - - +
382B ALA 3.4 0.4 - - - -
383B LEU* 1.3 73.3 - - - +
385B ARG* 1.3 65.6 + - - +
386B GLY 3.4 1.9 + - - -
387B VAL* 3.6 18.7 + - - +
389B ASN* 5.9 0.9 - - - +
392B PHE* 3.6 45.4 - - + +
428B SER* 4.8 5.4 - - - +
----------------------------------------------------------
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