Contacts of the helix formed by residues 315 - 325 (chain A) in PDB entry 3RC0
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 MET 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE 3.4 0.4 + - - -
314A GLN* 1.3 72.3 - - - +
316A VAL* 1.3 61.7 + - - +
318A VAL* 3.1 15.4 + - - +
319A ARG 3.3 4.2 + - - -
339A TRP* 3.1 23.3 - - + -
347A MET 3.9 17.5 - - - +
348A VAL* 3.8 3.1 - - + -
349A GLY* 3.5 32.5 - - - +
352A GLY* 3.0 35.5 + - - +
353A ALA* 3.6 26.2 - - - +
354A PHE* 3.6 34.1 - - + -
363A THR* 5.7 1.8 - - + -
366A GLU* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLN* 4.5 11.7 - - + -
315A MET* 1.3 75.1 - - - +
317A THR* 1.3 64.8 + - - +
319A ARG* 3.3 40.8 + - - +
320A GLU* 2.8 29.3 + - - +
339A TRP* 4.2 4.3 - - + -
349A GLY 4.7 0.2 - - - +
350A GLU* 3.6 43.0 + - + +
352A GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.5 1.6 - - + -
314A GLN* 3.0 33.6 + - - +
316A VAL* 1.3 78.1 - - - +
318A VAL* 1.3 58.0 + - - +
320A GLU* 3.3 13.3 + - - +
321A ALA* 2.9 26.9 + - - +
419A SER* 3.6 16.8 - - - +
422A LEU* 3.5 33.0 - - + +
423A THR* 3.9 10.4 + - - +
426A THR* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.0 10.8 - - + -
314A GLN 3.9 5.4 - - - +
315A MET 3.1 7.8 + - - +
317A THR* 1.3 73.8 - - - +
319A ARG* 1.3 66.0 + - - +
321A ALA* 3.2 4.7 + - - +
322A ALA* 3.0 20.7 + - - +
339A TRP* 5.1 0.9 - - + -
354A PHE* 3.4 33.7 - - + -
367A LEU* 5.3 4.0 - - + -
370A THR* 4.2 11.4 - - + -
371A LEU* 5.1 4.9 - - + -
374A LEU* 4.0 20.6 - - + -
415A LEU* 3.7 14.6 - - + +
416A LEU* 6.0 3.1 - - + -
419A SER* 3.4 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET 3.3 2.6 + - - -
316A VAL* 3.3 29.4 + - - +
318A VAL* 1.3 78.8 - - - +
320A GLU* 1.3 62.9 + - - +
322A ALA* 2.9 10.8 + - - +
323A LEU* 2.8 39.1 + - + +
335A VAL* 4.5 11.4 - - + -
336A TYR* 4.4 23.2 - - - -
339A TRP* 3.4 56.0 - - + +
350A GLU* 3.0 39.8 + - - -
374A LEU* 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL 2.8 16.5 + - - +
317A THR* 3.4 16.9 + - - +
319A ARG* 1.3 74.5 - - - +
321A ALA* 1.3 57.2 + - - +
323A LEU* 3.1 12.2 + - + +
324A GLN* 2.8 41.1 + - + +
422A LEU* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR 2.9 10.5 + - - +
318A VAL 3.2 8.9 + - - +
320A GLU* 1.3 75.7 - - - +
322A ALA* 1.3 60.5 + - - +
324A GLN* 3.4 9.6 + - - +
325A GLY* 3.4 16.8 + - - -
415A LEU* 3.8 11.1 - - + +
418A ASN* 4.0 17.6 + - + -
419A SER* 3.5 32.8 - - - +
422A LEU* 3.9 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL 3.0 11.7 + - - +
319A ARG* 2.9 12.7 + - - +
321A ALA* 1.3 74.1 - - - +
323A LEU* 1.3 64.9 + - - +
325A GLY* 3.4 9.9 + - - -
326A THR* 3.5 12.1 + - - +
335A VAL* 4.1 22.1 - - + +
374A LEU* 4.4 16.6 - - + +
415A LEU* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 2.8 31.6 + - + +
320A GLU* 3.6 11.0 - - + +
322A ALA* 1.3 70.3 - - - +
324A GLN* 1.3 67.2 + - - +
325A GLY 3.0 2.0 - - - -
326A THR* 2.7 29.1 + - - +
332A ARG* 3.9 16.1 - - + +
335A VAL* 3.4 31.2 - - + -
336A TYR* 3.2 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 2.8 32.2 + - + +
321A ALA* 3.5 8.5 - - - +
322A ALA 3.3 0.2 - - - -
323A LEU* 1.3 73.6 - - - +
325A GLY* 1.3 59.8 + - - +
326A THR 3.2 6.5 + - - +
418A ASN* 5.2 10.2 + - - +
422A LEU* 4.0 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA 3.4 6.7 + - - -
322A ALA 3.4 8.7 + - - -
323A LEU 3.0 1.2 + - - -
324A GLN* 1.3 77.9 - - - +
326A THR* 1.3 61.6 + - - +
327A LYS* 3.8 1.9 + - - +
418A ASN* 6.3 1.6 - - - -
----------------------------------------------------------
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