Contacts of the helix formed by residues 67 - 77 (chain P) in PDB entry 1HNW
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 THR 67 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A G 2.8 36.8 + - - +
377A G 4.4 12.0 + - - +
3P LYS* 5.0 7.1 - - - +
4P ILE 2.9 6.9 + - - -
5P ARG* 2.7 34.5 - - - +
65P GLN 3.7 0.6 + - - -
66P PRO* 1.3 79.8 - - - +
68P ASP* 1.3 80.7 + - + +
69P THR* 3.8 7.0 - - - +
70P ALA* 3.5 10.1 - - - +
71P ARG* 3.0 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A A 4.0 18.1 + - - +
454A C 3.8 37.6 + - - +
67P THR* 1.3 79.7 - - + +
69P THR* 1.3 66.5 + - - +
71P ARG* 2.8 29.5 + - - +
72P ARG* 2.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A U 2.4 34.9 + - - +
376A G 4.2 12.3 + - - -
452A A 4.8 4.7 - - - -
453A A 4.7 1.7 + - - -
6P LEU* 4.2 24.0 - - + -
39P TYR* 4.9 4.0 - - + -
67P THR* 3.4 2.0 - - - +
68P ASP* 1.3 78.6 - - - +
70P ALA* 1.3 67.1 + - - +
72P ARG* 2.8 42.7 + - - +
73P LEU* 3.0 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ILE* 2.9 43.3 - - + +
5P ARG* 3.8 7.9 - - - -
6P LEU* 3.8 13.5 - - + +
19P ILE* 5.5 1.8 - - + -
66P PRO* 4.2 0.4 - - + -
67P THR* 3.5 16.2 - - - +
68P ASP 3.2 0.6 - - - -
69P THR* 1.3 77.9 - - - +
71P ARG* 1.3 64.6 + - - +
73P LEU* 3.2 4.6 + - - +
74P LEU* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A C 5.8 5.2 - - - -
463A A 5.6 0.4 + - - -
60P LEU* 6.0 0.2 - - - +
65P GLN* 4.3 14.1 - - - +
66P PRO* 3.6 40.6 + - + +
67P THR 3.0 10.7 + - - +
68P ASP* 2.8 27.1 + - - +
70P ALA* 1.3 75.5 - - - +
72P ARG* 1.3 53.9 + - - +
74P LEU* 3.0 9.2 + - - +
75P ARG* 2.6 56.1 + - - +
80P PHE* 3.7 25.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
375A U 5.0 1.0 + - - -
451A A 4.3 8.9 - - - -
452A A 3.6 54.6 + - - -
453A A 3.3 49.8 + - - +
39P TYR* 3.3 24.0 + - - -
48P TRP* 5.8 1.6 - - - -
68P ASP 2.9 8.1 + - - +
69P THR* 2.8 37.5 + - - +
71P ARG* 1.3 74.0 - - - +
73P LEU* 1.3 79.0 + - - +
75P ARG* 3.6 10.4 - - - +
76P GLN* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P LEU* 4.4 11.2 - - + -
19P ILE* 3.8 21.5 - - + -
39P TYR* 3.4 53.2 - - + -
48P TRP* 6.0 0.2 - - + -
49P LEU* 4.0 20.9 - - + +
51P VAL* 4.9 0.9 - - - -
69P THR* 3.0 16.4 + - + +
70P ALA 3.7 4.3 - - - +
72P ARG* 1.3 102.8 - - - +
74P LEU* 1.3 70.0 + - - +
75P ARG 3.1 1.6 - - - -
76P GLN* 2.9 14.8 + - - +
77P ALA* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ILE* 4.2 28.9 - - + -
19P ILE* 4.2 26.9 - - + -
36P ILE* 5.3 1.1 - - + -
51P VAL* 4.1 17.7 - - + -
56P ALA* 4.3 8.5 - - + -
60P LEU* 4.6 5.2 - - + -
66P PRO* 4.9 3.8 - - + -
70P ALA 2.9 27.0 + - - +
71P ARG* 3.4 7.4 - - - +
73P LEU* 1.3 77.2 - - - +
75P ARG* 1.3 63.1 + - - +
77P ALA* 3.0 7.5 + - - +
79P VAL* 2.7 54.7 + - + +
80P PHE* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A C 5.3 8.9 + - - -
463A A 3.0 38.2 + - - -
474A G 2.5 45.5 + - - +
475A G 5.9 3.4 - - - +
71P ARG* 2.6 48.7 + - - +
72P ARG* 3.6 9.4 - - - +
74P LEU* 1.3 73.5 - - - +
76P GLN* 1.3 54.8 + - - +
78P GLY* 2.5 29.5 + - - +
79P VAL 4.4 0.2 - - - +
80P PHE* 3.4 24.0 - - + -
81P ARG* 4.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A A 5.9 3.0 + - - -
453A A 5.5 5.0 + - - +
48P TRP* 4.4 23.2 - - - -
49P LEU* 3.7 20.7 - - + +
72P ARG* 3.1 31.9 + - + +
73P LEU* 2.9 19.1 + - - +
75P ARG* 1.3 78.8 - - - +
77P ALA* 1.3 55.5 + - - +
78P GLY 3.2 2.3 + - - -
81P ARG* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P LEU* 4.8 4.9 - - + +
51P VAL* 3.5 41.1 - - + -
53P VAL* 3.1 19.6 - - + +
73P LEU 2.9 6.6 + - - +
74P LEU 3.2 7.6 - - - +
75P ARG 2.9 0.4 - - - -
76P GLN* 1.3 75.6 - - - +
78P GLY* 1.3 67.1 + - - +
79P VAL 3.1 0.2 + - - -
----------------------------------------------------------
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