Contacts of the helix formed by residues 62 - 73 (chain P) in PDB entry 3H1J
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 62 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 4.2 20.9 - - - +
61C SER* 5.2 1.6 - - - +
62C LEU* 4.2 19.1 - - + -
57P THR* 3.7 32.5 - - + -
59P ASP* 2.7 13.5 + - + +
61P SER* 1.3 90.6 + - - +
63P ALA* 1.3 65.5 + - - +
64P PHE 3.4 2.0 - - - -
65P SER* 3.1 14.7 + - - +
66P SER* 2.8 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P TYR* 3.5 24.0 - - - +
57P THR 3.3 12.3 + - - +
59P ASP 2.5 20.2 + - - +
60P THR 4.0 1.3 + - - +
62P LEU* 1.3 69.0 - - - +
64P PHE* 1.3 65.7 + - - +
66P SER* 2.7 22.8 + - - -
67P VAL* 3.2 11.2 + - - +
134P LEU 3.7 6.3 - - - +
135P PRO 4.1 1.6 - - - -
136P TRP* 3.9 9.0 - - + -
176P LEU* 3.6 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P THR 4.8 4.3 + - - +
62P LEU 3.4 0.6 - - - -
63P ALA* 1.3 78.5 - - - +
65P SER* 1.3 62.4 + - - +
67P VAL* 3.4 6.3 + - - +
68P ALA* 3.2 16.7 + - + +
135P PRO 3.1 25.6 + - - +
136P TRP* 3.7 18.9 - - + +
137P GLY* 4.4 0.4 - - - -
256P ASN 4.1 2.7 - - - -
257P PHE* 3.4 28.3 - - - -
258P THR 4.2 0.7 - - - -
259P PRO* 3.7 37.7 - - + -
3011P GOL 3.5 35.8 + - - -
45Q TYR* 3.4 32.3 - + - -
115Q TYR* 4.6 10.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P SER 4.1 5.0 + - - -
62P LEU* 3.1 28.4 + - - +
64P PHE* 1.3 78.3 - - - +
66P SER* 1.3 53.9 + - - +
68P ALA* 3.2 5.8 + - - +
69P HIS* 2.7 34.9 + - - +
45Q TYR* 3.7 28.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P HIS 3.8 16.9 - - - +
56P TYR* 3.5 7.6 - - - -
57P THR* 3.3 32.3 + - - -
62P LEU* 2.8 14.7 + - - -
63P ALA 2.7 18.4 + - - -
65P SER* 1.3 73.1 - - - +
67P VAL* 1.3 60.3 + - - +
69P HIS* 3.3 8.6 + - - +
70P THR* 2.8 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P TYR* 4.0 15.9 - - + +
63P ALA 3.2 15.9 + - - +
64P PHE 3.6 5.4 - - - +
65P SER 3.2 0.2 - - - -
66P SER* 1.3 78.3 - - - +
68P ALA* 1.3 65.4 + - - +
70P THR* 3.1 10.7 + - - -
71P CYS* 3.0 22.2 + - - -
81P ARG* 3.5 40.4 - - + +
135P PRO* 4.0 24.0 - - + -
501P HEM 4.0 18.6 - - + +
3011P GOL 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P PHE* 3.2 9.5 + - + +
65P SER 3.2 9.6 + - - +
67P VAL* 1.3 78.6 - - - +
69P HIS* 1.3 58.1 + - - +
71P CYS* 3.0 3.7 + - - +
72P ARG* 2.8 34.7 + - - +
3011P GOL 4.5 8.0 + - - +
45Q TYR* 3.5 28.9 - - + -
115Q TYR* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P HIS* 4.6 13.9 + + + +
65P SER 2.7 20.0 + - - +
66P SER* 3.6 9.6 + - - +
68P ALA* 1.3 72.0 - - - +
70P THR* 1.3 62.0 + - - +
72P ARG* 4.4 2.0 - - - +
73P ASN* 2.6 63.3 + - + +
74P VAL* 3.3 26.6 + - + +
45Q TYR* 5.3 1.1 - - - -
65R SER* 3.7 5.5 + - - -
67R ASP* 2.9 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 3.9 29.5 + - + -
55P HIS* 3.2 30.0 + - + +
56P TYR* 5.2 0.2 - - - -
66P SER 2.8 18.4 + - - -
67P VAL* 3.2 14.6 - - - -
69P HIS* 1.3 78.3 + - - +
71P CYS* 1.3 63.9 + - - +
74P VAL* 3.0 38.8 + - + +
77P GLY* 3.2 20.4 - - - +
81P ARG* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P VAL 3.0 10.4 + - - -
68P ALA 3.0 7.4 + - - +
70P THR* 1.3 83.3 - - - +
72P ARG* 1.3 64.7 + - + +
74P VAL 4.4 2.9 - - - +
78P TRP* 3.6 41.3 + - + +
81P ARG* 3.4 51.6 - - - -
82P ASN* 5.7 2.0 - - - -
3011P GOL 4.1 9.2 - - - +
115Q TYR* 5.0 1.3 - - + +
197Q GLU* 5.2 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P ALA* 2.8 22.5 + - - +
69P HIS* 4.3 0.9 - - - +
71P CYS* 1.3 78.3 - - + +
73P ASN* 1.3 70.5 + - - +
74P VAL 5.2 0.2 - - - -
45Q TYR* 3.4 45.3 + - - +
46Q VAL* 4.3 5.7 - - - +
49Q ARG* 5.5 0.3 + - - -
50Q ASN* 5.3 7.2 - - - +
114Q SER* 3.7 12.1 + - - -
115Q TYR* 2.5 48.6 + - - +
193Q ALA 2.6 30.1 + - - -
194Q ALA* 3.8 4.2 - - - +
196Q PRO* 4.0 21.1 - - + +
197Q GLU* 6.2 0.2 - - - +
66R ALA* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P HIS* 2.6 47.9 + - + +
72P ARG* 1.3 84.6 - - - +
74P VAL* 1.3 63.7 + - - +
75P GLN* 3.3 4.5 + - - +
49Q ARG* 3.0 27.2 + - - -
50Q ASN* 5.4 0.5 - - - +
90Q TYR* 3.8 11.4 + - - -
65R SER* 3.1 3.6 - - - -
66R ALA* 3.0 25.7 + - - +
67R ASP* 3.3 36.5 + - - +
----------------------------------------------------------
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