Contacts of the helix formed by residues 316 - 330 (chain B) in PDB entry 3C3C
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 316 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASP* 2.9 33.5 + - - +
285B PHE* 3.5 9.1 - - - +
286B VAL* 4.5 5.2 - - - -
315B CYS* 1.3 77.2 - - - +
317B PRO* 1.3 69.2 - - - +
319B SER* 3.6 0.5 + - - -
320B SER* 3.1 25.3 + - - -
350B GLY* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASP* 3.3 11.2 - - - +
286B VAL* 6.1 0.4 - - + -
316B GLY* 1.3 82.0 - - - +
318B GLU* 1.3 60.0 + - - +
320B SER* 3.3 11.1 - - - -
321B LYS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.7 17.7 - - + -
284B ASP* 3.0 17.8 + - - +
317B PRO* 1.3 75.8 - - - +
319B SER* 1.3 66.0 + - - +
321B LYS* 2.9 28.2 + - - +
322B LYS* 2.8 37.5 + - + +
325B GLU* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PRO* 3.4 8.7 - - - -
283B VAL* 2.5 35.8 + - - +
284B ASP* 2.6 34.2 + - - -
315B CYS* 3.6 23.3 - - - -
316B GLY 3.7 0.2 - - - -
318B GLU* 1.3 71.8 - - - +
320B SER* 1.3 64.1 + - - +
322B LYS* 3.0 9.3 + - - +
323B TYR* 2.9 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B CYS* 4.3 9.7 - - - -
316B GLY 3.1 16.1 + - - -
317B PRO* 3.3 15.6 - - - +
319B SER* 1.3 76.7 - - - +
321B LYS* 1.3 60.7 + - - -
323B TYR* 3.4 10.6 + - - +
324B ALA* 3.1 24.8 + - - +
350B GLY* 4.4 7.1 + - - -
353B ALA* 3.8 25.5 - - - +
354B LEU 5.3 0.3 + - - -
357B GLU* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 2.9 15.3 + - - +
318B GLU* 2.9 37.5 + - - +
320B SER* 1.3 69.6 - - - +
322B LYS* 1.3 65.1 + - - +
324B ALA* 3.4 7.0 + - - +
325B GLU* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 4.2 22.5 - - + +
281B LEU 4.5 6.5 - - - +
283B VAL* 3.8 34.5 - - + -
318B GLU* 2.8 28.0 + - + +
319B SER* 3.4 11.2 - - - +
321B LYS* 1.3 76.9 - - - +
323B TYR* 1.3 64.0 + - + +
325B GLU* 3.3 30.9 + - - +
326B ALA* 3.4 7.8 + - - +
329B ARG* 5.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 3.4 45.7 - - + +
236B GLY* 3.8 12.6 - - - -
237B GLY 4.9 0.3 + - - -
280B THR* 4.4 6.1 - - + -
281B LEU 4.2 19.5 - - - -
282B PRO* 3.4 32.3 - - + +
315B CYS* 3.7 26.2 - - - +
319B SER* 2.9 22.3 + - - +
320B SER* 3.7 10.1 - - - +
322B LYS* 1.3 77.7 - - + +
324B ALA* 1.3 57.5 + - - +
326B ALA* 3.1 19.6 + - - +
327B VAL* 3.1 18.3 + - - +
339B VAL* 4.3 15.8 + - + +
350B GLY 5.5 0.7 - - - -
354B LEU* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER 3.1 15.8 + - - +
321B LYS* 3.6 8.3 - - - +
323B TYR* 1.3 77.3 - - - +
325B GLU* 1.3 63.9 + - + +
327B VAL* 3.2 11.5 + - - +
328B THR* 3.1 28.4 + - - +
357B GLU* 3.7 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 5.7 0.5 - - - +
321B LYS* 3.1 21.5 + - - +
322B LYS* 3.3 27.2 + - - +
324B ALA* 1.3 76.7 - - - +
326B ALA* 1.3 60.6 + - - +
328B THR* 2.8 21.6 + - - +
329B ARG* 3.1 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.0 14.0 - - + +
232B GLU* 3.7 20.2 - - - +
234B ILE* 4.2 18.4 - - + -
280B THR* 4.7 4.3 - - - +
322B LYS 3.4 8.0 + - - +
323B TYR 3.1 11.5 + - - +
325B GLU* 1.3 78.8 - - - +
327B VAL* 1.3 60.9 + - - +
329B ARG* 3.2 26.6 + - - +
330B ALA* 3.3 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.3 13.5 - - + -
210B ILE* 5.1 2.7 - - + -
234B ILE* 5.2 0.4 - - + -
323B TYR 3.1 18.8 + - - +
324B ALA* 3.2 9.8 + - - +
326B ALA* 1.3 75.6 - - - +
328B THR* 1.3 61.5 + - + +
329B ARG 3.3 0.2 + - - -
330B ALA* 3.5 6.6 + - - +
333B ILE* 3.5 24.4 - - + +
354B LEU* 3.9 24.7 - - + -
357B GLU* 3.5 33.2 - - + +
358B VAL* 4.5 2.5 - - + -
361B ALA* 3.6 6.9 - - + +
364B ARG* 2.8 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA 3.1 15.1 + - - +
325B GLU* 2.8 22.7 + - - +
327B VAL* 1.3 74.7 - - - +
329B ARG* 1.3 62.1 + - - +
357B GLU* 5.1 8.3 - - - +
364B ARG* 3.5 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO* 3.8 23.9 - - + +
232B GLU* 2.9 43.4 + - - +
278B LYS* 4.9 9.3 - - - +
280B THR* 4.6 6.7 + - - +
322B LYS 5.2 1.2 + - - -
325B GLU* 3.1 38.5 + - - +
326B ALA* 3.2 18.9 + - - +
327B VAL 3.1 0.6 - - - -
328B THR* 1.3 80.8 - - - +
330B ALA* 1.3 62.8 + - - +
331B LYS* 3.8 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO* 3.7 11.9 - - + +
208B LEU* 3.8 29.8 - - + +
326B ALA 3.3 9.5 + - - +
327B VAL 3.5 4.8 + - - +
329B ARG* 1.3 79.3 - - - +
331B LYS* 1.3 60.7 + - - +
332B GLN 4.1 1.8 - - - +
333B ILE* 3.9 19.7 - - + -
364B ARG* 2.7 32.6 + - - -
366B CYS* 3.6 3.4 - - - -
----------------------------------------------------------
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