Contacts of the helix formed by residues 58 - 69 (chain y) in PDB entry 3J45
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 58 (chain y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56y GLN* 3.3 17.7 - - - +
57y ARG* 1.3 84.6 - - - +
59y THR* 1.4 63.3 + - - +
60y ILE* 3.0 9.8 + - - -
61y ILE* 3.2 24.4 + - - +
62y GLU 3.7 2.4 + - - -
292y SER* 5.1 3.6 - - - -
304y THR* 6.6 0.2 - - - -
308y LEU* 5.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56y GLN* 3.4 17.0 + - - +
58y GLY* 1.4 69.9 - - - -
60y ILE* 1.4 63.0 + - - +
62y GLU* 3.1 22.5 + - - +
63y MET* 3.6 15.8 + - - +
308y LEU* 4.3 15.6 - - - +
312y PRO 3.7 22.0 + - - +
313y GLY* 5.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58y GLY 4.7 1.1 - - - -
59y THR* 1.4 76.5 - - - +
61y ILE* 1.4 62.8 + - - +
62y GLU 3.3 0.7 + - - -
63y MET* 3.5 13.9 + - + +
64y PHE* 3.4 18.9 + - - +
285y LEU* 4.6 6.6 - - + +
288y ALA* 3.5 30.1 - - + +
289y THR* 3.6 18.6 - - - +
292y SER* 3.5 17.3 - - - +
307y SER* 4.0 23.8 - - - +
308y LEU* 4.0 23.8 - - + +
311y GLN* 3.8 31.2 - - + -
312y PRO 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53y LEU* 4.3 23.8 - - + +
56y GLN* 6.0 2.5 - - + -
57y ARG* 3.4 56.5 - - + +
58y GLY 3.2 10.9 + - - +
60y ILE* 1.4 72.2 - - - +
62y GLU* 1.3 61.9 - - - +
64y PHE* 3.3 5.4 + - + +
65y ASN* 3.2 22.2 + - + +
72y LEU* 5.0 6.7 - - + +
289y THR* 4.1 8.7 - - - +
292y SER* 3.9 18.2 - - - -
293y TRP* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56y GLN* 3.8 31.7 + - + +
58y GLY 3.7 2.0 + - - +
59y THR* 3.1 17.3 + - - +
61y ILE* 1.3 76.9 - - - +
63y MET* 1.4 64.9 + - + +
65y ASN* 3.4 9.7 - - + +
66y MET* 3.3 25.3 + - - +
399y PHE* 4.5 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59y THR* 3.6 8.3 + - - +
60y ILE* 3.5 26.8 + - + +
62y GLU* 1.4 75.8 - - + +
64y PHE* 1.3 59.6 + - - +
66y MET* 3.0 34.3 + - + +
67y PHE* 3.5 17.9 - - + -
285y LEU* 3.8 36.6 - - + -
311y GLN* 3.8 23.6 - - + -
312y PRO* 4.2 31.2 - - + +
321y TYR* 5.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60y ILE 3.4 6.8 + - - +
61y ILE* 3.6 6.5 - - + +
62y GLU 3.2 0.4 - - - -
63y MET* 1.3 80.8 - - - +
65y ASN* 1.3 57.4 + - - +
67y PHE* 3.8 2.7 + - - +
68y SER* 3.3 37.3 + - - -
72y LEU* 3.6 23.3 - - + -
79y ALA 4.8 2.7 - - - -
80y LEU* 3.9 13.5 - - - -
83y MET* 3.6 41.3 - - + -
131y GLN* 4.2 12.8 - - - -
285y LEU* 4.0 15.7 - - + +
286y PHE* 4.9 9.9 - + - -
289y THR* 3.2 46.7 - - + +
293y TRP* 3.9 16.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53y LEU* 4.8 7.7 - - - +
61y ILE* 3.2 14.4 + - + +
62y GLU* 3.4 14.7 - - - +
64y PHE* 1.3 73.9 - - - +
66y MET* 1.4 58.5 + - - +
68y SER* 4.7 0.2 - - - -
69y GLY* 2.8 35.0 + - - +
72y LEU* 3.5 25.4 + - + +
73y SER* 3.0 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62y GLU* 3.3 12.9 + - + +
63y MET* 3.0 32.5 - - + +
65y ASN* 1.4 75.5 + - - +
67y PHE* 1.4 71.1 + - + +
69y GLY* 3.8 7.4 + - - -
194y GLY 4.9 0.2 - - - +
195y ILE* 3.0 36.1 - - + +
399y PHE* 6.3 3.4 - - - -
404y THR* 3.8 34.3 - - + -
405y SER* 4.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63y MET* 3.5 23.4 + - + -
64y PHE 4.1 1.3 - - - +
66y MET* 1.4 82.5 - - + +
68y SER* 1.3 60.5 + - - +
69y GLY* 3.6 0.9 + - - -
82y ILE* 5.9 0.2 - - - +
83y MET* 3.6 28.3 - - + -
190y ILE* 4.5 1.4 - - - +
191y ILE* 3.7 56.4 - - + +
195y ILE* 4.4 6.5 - - + -
278y ILE* 6.4 0.7 - - - -
281y SER* 4.0 27.8 - - - -
285y LEU* 3.9 24.5 - - + -
321y TYR* 5.3 4.3 - - - -
404y THR* 3.7 30.5 - - + -
408y ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33y PHE* 3.7 22.0 - - - -
64y PHE* 3.3 23.2 + - - -
65y ASN 4.3 1.3 - - - -
67y PHE* 1.3 76.6 - - - +
69y GLY* 1.4 57.8 - - - +
71y ALA* 4.6 3.3 - - - +
72y LEU* 4.7 8.3 - - - -
78y PHE 4.5 6.2 - - - +
79y ALA 3.7 17.9 + - - -
80y LEU 3.4 20.5 + - - -
81y GLY* 4.7 3.2 - - - -
82y ILE* 6.2 1.3 - - - -
83y MET* 3.6 15.4 - - - +
190y ILE* 4.7 9.6 - - - +
194y GLY* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33y PHE* 5.0 0.7 - - - -
65y ASN* 2.8 26.9 + - - +
66y MET* 4.1 4.0 - - - -
67y PHE 3.4 0.4 - - - -
68y SER* 1.4 62.4 - - - +
70y GLY* 1.4 57.3 + - - -
71y ALA 3.3 7.8 + - - -
72y LEU* 3.8 1.7 + - - +
73y SER* 3.7 8.7 + - - -
194y GLY* 3.6 29.2 - - - -
----------------------------------------------------------
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