Contacts of the helix formed by residues 315 - 327 (chain A) in PDB entry 4XNW
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 LEU 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 4.6 12.3 - - + -
61A VAL* 3.8 23.1 - - + -
271A VAL* 4.4 11.9 - - + -
272A SER* 3.8 5.2 - - - +
311A GLY 4.3 8.3 - - - +
312A LEU* 3.3 40.2 + - + +
314A SER* 1.3 73.4 - - - +
316A ASN* 1.3 65.4 + - - +
317A SER 3.1 3.4 + - - -
318A CYS* 3.2 18.4 + - - -
319A VAL* 3.2 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 3.3 25.5 + - - -
100A TYR* 6.5 0.2 - - - -
134A ASN* 3.9 13.4 + - - +
135A LEU* 5.9 0.7 - - - +
138A SER* 4.0 4.4 + - - -
268A VAL* 4.2 17.0 - - + -
272A SER* 4.1 5.8 + - - -
273A TYR* 3.3 34.5 + - + +
313A ALA 2.4 29.3 + - - +
314A SER* 4.2 0.7 - - - -
315A LEU* 1.3 77.9 - - - +
317A SER* 1.3 60.9 + - - +
319A VAL* 4.5 4.9 - - - +
320A ASN* 2.8 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.8 3.8 - - - -
65A GLY* 3.7 5.3 - - - -
69A ASN* 2.7 29.6 + - - -
97A ASP* 2.8 30.0 + - - +
100A TYR* 3.4 23.7 - - - -
101A VAL* 4.0 21.3 - - - -
314A SER 3.4 11.9 + - - -
315A LEU 3.1 1.6 - - - -
316A ASN* 1.3 81.0 + - - +
318A CYS* 1.3 57.3 + - - +
319A VAL 3.6 0.2 - - - -
321A PRO* 3.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.1 35.4 - - - -
64A ILE* 3.7 35.2 - - + +
65A GLY* 3.8 12.1 - - - +
315A LEU* 3.8 14.8 - - - -
317A SER* 1.3 77.2 - - - +
319A VAL* 1.3 65.3 + - - +
320A ASN 3.7 0.2 - - - -
321A PRO* 3.9 10.8 - - - +
322A ILE* 3.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.7 11.3 - - + +
268A VAL* 4.2 21.8 - - + -
315A LEU* 3.3 24.5 - - + +
316A ASN* 3.2 6.4 + - - +
318A CYS* 1.3 85.4 - - - +
320A ASN* 1.3 65.7 + - - +
321A PRO* 3.3 2.9 - - - -
322A ILE* 3.2 27.5 + - + +
323A LEU* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.2 17.4 - - - +
97A ASP* 2.8 29.1 + - - +
138A SER* 4.7 1.0 + - - -
142A LEU* 5.1 7.0 - - - +
264A ILE* 5.6 1.0 - - - +
268A VAL* 4.5 13.0 - - - +
273A TYR* 4.9 1.8 + - - -
316A ASN* 2.8 41.5 + - - +
319A VAL* 1.3 76.8 - - - +
321A PRO* 1.3 59.3 - - + +
323A LEU* 2.6 51.2 + - + +
324A TYR* 3.3 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 4.0 32.3 - - - +
69A ASN* 3.8 22.0 - - - +
72A ALA* 5.5 0.7 - - + -
317A SER 3.9 9.2 - - - +
318A CYS* 3.9 8.7 - - - +
319A VAL 3.4 7.9 - - - +
320A ASN* 1.3 94.7 - - + +
322A ILE* 1.3 66.2 + - + +
324A TYR* 3.3 25.8 + - + +
325A PHE* 3.5 17.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.5 9.0 - - + -
318A CYS 3.9 17.0 - - - +
319A VAL* 3.2 22.9 + - + +
320A ASN 3.2 1.0 - - - -
321A PRO* 1.3 75.7 - - + +
323A LEU* 1.3 65.7 + - - +
325A PHE* 3.2 10.8 + - + +
326A LEU* 2.9 49.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
90A MET* 4.0 13.8 - - + +
93A LEU* 4.8 7.9 - - + -
142A LEU* 3.6 29.8 - - + -
145A ILE* 5.4 0.2 - - + -
261A LEU* 4.2 15.0 - - + -
264A ILE* 3.8 37.7 - - + +
265A VAL* 4.3 8.3 - - + -
319A VAL 3.8 1.6 + - - -
320A ASN* 2.6 35.6 + - + +
322A ILE* 1.3 72.1 - - - +
324A TYR* 1.3 61.5 + - + +
327A ALA* 2.8 51.1 + - + +
328A GLY 3.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 3.5 19.1 + - - -
72A ALA* 3.5 23.3 - - + -
76A PHE* 4.0 22.1 - + + -
90A MET* 3.8 38.3 - - + +
93A LEU* 3.3 19.5 - - + +
94A ALA* 3.0 36.2 + - + -
97A ASP* 3.3 14.6 + - - -
320A ASN* 3.6 17.7 - - + +
321A PRO* 3.3 20.9 + - + +
323A LEU* 1.3 79.1 - - + +
325A PHE* 1.3 62.5 + - + +
328A GLY* 3.6 16.3 + - - -
329A ASP 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 5.8 1.8 - - + -
75A MET* 5.9 5.6 - - + -
257A LYS* 5.7 0.9 - - - -
321A PRO* 3.5 16.6 + - + -
322A ILE* 3.2 12.5 + - + +
323A LEU 3.1 0.2 - - - -
324A TYR* 1.3 82.7 - - + +
326A LEU* 1.3 71.1 + - + +
327A ALA 3.6 0.2 + - - -
328A GLY 4.1 8.3 + - - +
329A ASP 5.2 1.6 - - - +
330A THR* 6.1 0.9 - - - +
49C PHE* 4.1 27.8 - + + -
53C TYR* 3.5 48.2 - + + -
308C VAL* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 5.6 1.4 - - - -
257A LYS* 3.6 16.3 - - - +
260A TYR* 3.7 58.5 - - + +
264A ILE* 4.5 7.6 - - + -
322A ILE* 2.9 39.2 + - + +
325A PHE* 1.3 83.6 - - + +
327A ALA* 1.3 58.6 + - - +
305C THR* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 4.7 0.2 - - - +
90A MET* 3.9 10.1 - - + +
145A ILE* 6.0 0.5 - - - +
149A ARG* 2.7 31.7 + - - -
257A LYS* 3.7 24.6 - - - +
260A TYR* 4.5 1.3 - - + -
261A LEU* 3.9 15.2 - - + +
323A LEU* 2.8 35.9 + - + +
326A LEU* 1.3 76.5 - - - +
328A GLY* 1.3 56.4 + - - +
----------------------------------------------------------
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