Contacts of the helix formed by residues 364 - 369 (chain A) in PDB entry 5M64
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 PRO 364 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.0 15.7 - - + +
55A GLY* 5.7 0.4 - - - -
73A PRO 4.9 0.7 - - - +
74A GLY* 4.1 15.0 - - - -
75A HIS 3.4 26.0 - - - +
76A GLN* 5.5 1.1 - - - +
362A VAL 4.4 0.7 - - - +
363A PRO* 1.3 89.6 - - + +
365A THR* 1.3 64.9 + - - +
366A ARG* 4.2 18.4 - - - +
367A PHE* 3.0 25.3 + - + +
368A ARG* 3.1 11.8 + - - +
1111B LEU* 5.2 12.1 - - + +
1187B SER* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.6 31.1 - - + -
51A ASP 3.9 8.0 + - - -
54A LEU* 3.7 19.0 + - - +
55A GLY* 4.6 5.6 - - - -
56A ALA 3.9 10.1 - - - +
57A PHE* 3.6 34.5 - - + -
364A PRO* 1.3 73.1 - - - +
366A ARG* 1.3 58.5 + - - +
368A ARG* 2.9 44.3 + - - +
369A LEU* 3.3 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 5.6 2.3 - - - -
56A ALA 4.2 13.1 + - - +
69A GLU* 5.2 18.6 - - + +
72A CYS 4.7 8.5 + - - +
73A PRO* 2.5 37.4 + - - -
74A GLY* 3.9 6.1 - - - +
364A PRO* 3.2 10.7 - - + +
365A THR* 1.3 79.6 - - - +
367A PHE* 1.3 102.8 + - - +
368A ARG 3.6 0.3 + - - -
369A LEU* 4.1 16.4 + - - +
1054B SER* 4.4 18.0 - - - +
1055B LEU* 5.2 0.3 - - - -
1057B MET* 6.0 7.7 - - - +
1111B LEU* 6.4 0.2 - - - +
1180B PHE* 6.0 1.8 - - - -
1183B LYS* 3.3 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 4.8 4.9 - - + -
364A PRO* 3.0 30.4 + - + +
366A ARG* 1.3 117.4 - - - +
368A ARG* 1.3 61.4 + - - +
369A LEU 3.5 1.9 + - - -
380A ASN* 4.3 5.5 + - - -
1054B SER 4.5 3.6 - - - -
1055B LEU* 3.4 49.3 - - - +
1056B THR* 5.4 1.6 - - - -
1180B PHE* 4.2 8.1 - - + -
1183B LYS* 3.2 28.0 - - + -
1184B TYR* 3.6 47.5 - + + -
1187B SER* 4.3 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.3 28.7 + - - +
50A TYR* 2.5 50.2 + - - +
54A LEU* 3.4 9.3 - - - +
362A VAL* 5.0 2.7 - - - -
363A PRO* 2.5 54.3 + - + -
364A PRO 3.1 6.4 + - - +
365A THR* 2.9 37.5 + - - +
367A PHE* 1.3 80.1 - - - +
369A LEU* 1.3 60.8 + - - +
380A ASN* 3.8 26.4 - - + +
382A GLN* 4.4 6.5 - - - +
383A ASN* 3.0 28.4 - - - +
386A LEU* 5.0 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.5 15.7 - - + -
58A LEU* 5.2 7.2 - - - +
69A GLU* 5.3 8.5 - - - +
365A THR 3.3 6.1 + - - +
366A ARG* 4.2 13.9 - - - +
367A PHE 3.5 3.0 + - - -
368A ARG* 1.3 77.2 - - - +
370A PRO* 1.3 105.4 - - + +
371A SER* 3.1 8.4 + - - -
380A ASN* 4.5 8.0 - - - +
1054B SER* 4.9 14.8 - - - +
1055B LEU* 4.6 21.2 - - + +
----------------------------------------------------------
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