Contacts of the helix formed by residues 314 - 325 (chain A) in PDB entry 2CSX
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 314 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL 2.8 22.7 + - - -
313A TYR* 1.3 71.9 - - - +
315A LEU* 1.3 63.9 + - - -
317A GLU* 3.0 14.3 - - - +
318A VAL* 2.8 28.5 + - - +
495A ARG* 3.8 13.6 - - - +
489B LYS* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 5.5 0.9 - - + -
86A PHE 4.2 4.5 - - - +
87A LEU* 3.7 42.4 - - + +
88A LYS* 3.4 28.0 - - + -
310A VAL* 3.9 22.4 - - + +
314A GLY* 1.3 70.4 - - - +
316A ASP* 1.3 72.5 + - - +
317A GLU* 2.9 2.6 + - - -
318A VAL* 3.0 4.2 + - + +
319A ARG* 2.9 36.1 + - + +
457A ASN* 3.4 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 1.3 80.4 - - - +
317A GLU* 1.3 59.4 + - - +
319A ARG* 3.7 10.7 - - - +
320A TYR* 2.7 33.5 + - - +
454A ILE 4.7 0.3 - - - +
455A THR* 2.8 48.0 + - - +
456A PRO* 3.2 1.4 - - - +
457A ASN* 2.9 33.9 + - - +
458A LYS* 3.2 34.7 - - + +
492A PHE* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR 3.0 28.6 - - - +
314A GLY* 3.0 20.0 - - - +
315A LEU 2.9 2.2 + - - -
316A ASP* 1.3 81.6 + - - +
318A VAL* 1.3 57.3 + - - +
320A TYR* 3.1 4.5 + - - +
321A PHE* 2.8 27.5 + - - +
343A ILE* 3.4 36.3 - - + +
347A LEU* 4.1 16.4 - - + +
458A LYS* 3.7 30.3 + - - -
492A PHE* 3.9 13.3 - - + +
493A PRO* 5.0 5.7 - - - +
495A ARG* 5.0 7.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
22A LEU* 5.6 2.0 - - + -
25A ALA* 6.5 0.2 - - + -
29A ILE* 4.6 8.5 - - + -
309A VAL* 4.1 28.9 - - + +
310A VAL* 4.2 18.6 - - + -
313A TYR* 4.2 11.0 - - + -
314A GLY 2.8 19.3 - - - +
315A LEU* 3.0 4.9 + - + +
317A GLU* 1.3 71.4 - - - +
319A ARG* 1.3 71.2 + - + +
321A PHE* 4.2 7.6 - - - -
322A LEU* 2.9 43.2 + - + +
334A PHE* 5.0 12.8 - - + -
339A ILE* 5.4 2.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
29A ILE* 3.7 43.3 - - + +
32A ASP* 2.5 37.9 + - - +
33A THR* 3.2 14.6 - - - +
36A ARG* 3.9 2.2 - - - +
87A LEU* 4.3 13.1 + - - -
89A ILE* 5.0 1.4 - - - +
315A LEU* 2.9 35.7 + - + +
316A ASP* 3.7 7.9 - - - +
318A VAL* 1.3 81.1 - - - +
320A TYR* 1.3 65.0 + - - +
322A LEU* 3.6 2.0 - - - +
323A LEU* 3.2 26.6 + - - +
453A PRO 3.0 27.1 + - - -
454A ILE* 2.9 25.0 + - - +
456A PRO* 3.5 19.9 - - - +
457A ASN* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP 2.7 18.9 + - - +
317A GLU 3.2 4.0 - - - +
319A ARG* 1.3 73.9 - - - +
321A PHE* 1.3 73.5 + - + +
323A LEU* 3.1 2.9 + - - +
324A ARG* 3.0 41.9 + - + +
342A ARG* 4.4 11.4 - - + -
343A ILE* 6.4 0.4 - - + -
346A GLU* 2.8 36.8 + - - +
347A LEU* 3.5 40.8 - - + -
351A ILE* 4.5 8.5 - - + -
402A ILE* 4.0 14.8 - - + -
405A ILE* 6.0 0.2 - - + -
406A LEU* 3.6 17.3 - - + +
451A LEU* 5.1 9.4 - - + -
454A ILE* 3.3 32.8 - - + +
455A THR* 5.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TRP* 3.8 13.9 - + - -
317A GLU 2.8 19.7 + - - +
318A VAL* 3.9 6.5 - - - +
320A TYR* 1.3 81.4 - - + +
322A LEU* 1.3 59.3 + - + +
324A ARG* 4.9 0.7 - - - -
325A GLU* 3.0 75.1 + - + +
333A ASP 3.7 13.2 - - - -
334A PHE* 3.5 39.7 - + - -
338A ALA* 4.1 4.5 - - + -
339A ILE* 3.8 42.0 - - + -
342A ARG* 3.7 20.9 - - + -
343A ILE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.4 16.8 - - + -
25A ALA* 4.9 0.9 - - + -
26A TYR* 3.5 37.1 + - + +
29A ILE* 3.9 27.4 - - + -
289A TRP* 3.4 57.3 - - + +
318A VAL* 2.9 33.6 + - + +
319A ARG* 3.6 3.8 - - - +
321A PHE* 1.3 77.4 - - - +
323A LEU* 1.3 61.3 + - + +
324A ARG 3.7 0.2 + - - -
325A GLU 4.6 1.4 + - - -
326A VAL* 4.7 3.5 - - - +
334A PHE* 4.2 19.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
26A TYR* 4.5 11.4 - - + -
29A ILE* 4.5 6.7 - - + -
30A ALA* 4.1 25.4 - - + +
33A THR* 3.2 31.4 - - + +
319A ARG 3.2 15.9 + - - +
320A TYR 3.1 2.5 + - - +
322A LEU* 1.3 79.5 - - + +
324A ARG* 1.3 59.8 + - - +
326A VAL 4.1 6.1 - - - +
328A PHE* 5.3 1.0 - - + +
398A PHE* 3.5 43.4 - - + +
399A TYR* 3.8 7.4 + - - -
402A ILE* 3.4 19.8 - - + +
454A ILE* 3.7 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.0 30.0 + - + +
321A PHE* 4.8 1.3 - - - +
323A LEU* 1.3 78.9 - - - +
325A GLU* 1.3 75.3 + - - +
326A VAL 3.4 2.5 - - - -
342A ARG* 2.5 52.1 - - - +
346A GLU* 2.7 31.5 + - - -
399A TYR* 3.1 30.3 + - - +
402A ILE* 3.5 36.3 - - + -
406A LEU* 4.5 7.2 - - + +
24C G 5.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TRP* 4.3 11.4 - - + -
321A PHE* 3.0 52.5 + - + +
322A LEU 4.6 0.4 + - - -
324A ARG* 1.3 83.5 + - - +
326A VAL* 1.3 59.5 + - + +
327A PRO* 4.6 0.3 - - - +
332A GLY* 6.3 0.2 - - - -
333A ASP 4.7 8.5 - - - +
338A ALA* 3.6 15.4 - - - +
342A ARG* 2.8 37.7 + - - +
399A TYR* 3.6 9.2 - - - -
----------------------------------------------------------
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