Contacts of the helix formed by residues 45 - 56 (chain S) in PDB entry 2HQT
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 HIS 45 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S TRP* 3.8 18.4 - - + -
36S VAL* 3.7 31.7 - - + +
41S GLN* 2.8 37.6 + - + +
42S ILE* 2.9 10.0 + - - +
44S PRO* 1.3 79.8 - - + +
46S LEU* 1.3 58.7 + - - +
47S ASP 3.3 2.7 - - - -
48S GLN* 2.9 31.7 + - - +
49S LEU* 2.8 29.4 + - - +
88T LYS* 3.7 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ILE* 3.0 27.0 + - + -
43S GLN* 3.1 30.1 + - + +
45S HIS* 1.3 77.2 - - - +
47S ASP* 1.3 64.9 + - - +
49S LEU* 3.1 13.8 + - + +
50S ASN* 3.0 19.9 + - - +
76S ALA* 4.8 9.2 - - + -
79S LEU* 4.9 8.7 - - + -
80S ILE* 4.3 10.8 - - + -
83S LEU* 3.7 30.3 - - + -
97S TYR* 4.2 13.2 - - + +
100S ILE* 3.4 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S GLN 4.8 0.2 + - - -
44S PRO 4.8 4.8 + - - +
45S HIS 3.3 0.6 - - - -
46S LEU* 1.3 77.9 - - - +
48S GLN* 1.3 58.3 + - - +
50S ASN* 3.3 8.6 + - - +
51S LEU* 3.0 22.7 + - - +
96S THR 5.4 0.7 - - - +
97S TYR* 3.8 21.8 + - - -
92T SER* 3.5 23.7 - - - +
93T THR* 4.7 8.4 + - - +
95T THR* 5.5 0.3 + - - -
96T THR* 3.5 39.3 + - - +
97T TYR* 4.7 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S TRP* 4.0 15.7 - - + -
36S VAL* 5.4 0.5 - - - +
44S PRO 5.4 0.2 + - - -
45S HIS* 2.9 42.4 + - - +
47S ASP* 1.3 75.8 - - - +
49S LEU* 1.3 61.7 + - - +
51S LEU* 3.2 2.4 + - + +
52S VAL* 2.8 40.8 + - + +
88T LYS* 4.3 7.3 + - + -
89T ASP* 3.1 41.3 + - + +
92T SER* 3.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S TRP* 3.8 25.1 - - + -
42S ILE* 5.6 1.3 - - + -
45S HIS 2.8 13.3 + - - +
46S LEU* 3.1 15.5 + - + +
48S GLN* 1.3 76.0 - - - +
50S ASN* 1.3 65.8 + - - +
52S VAL* 3.3 3.0 + - + +
53S LEU* 3.0 39.7 + - + +
59S ILE* 3.7 32.3 - - + -
72S VAL* 3.7 22.2 - - + -
76S ALA* 4.3 10.3 - - + -
100S ILE* 4.1 17.5 - - + -
103S TRP* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S LEU 3.0 12.3 + - - +
47S ASP* 3.6 11.7 - - - +
49S LEU* 1.3 76.8 - - - +
51S LEU* 1.3 61.7 + - - +
54S ARG 3.1 16.8 + - - -
96S THR 3.3 22.4 - - - +
97S TYR* 3.2 13.9 - - + +
98S ARG 4.2 0.5 + - - -
99S HIS* 3.0 60.6 - - - +
100S ILE* 3.1 21.6 - - + +
96T THR* 5.6 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S ASP 3.0 15.8 + - - +
48S GLN* 3.8 4.7 - - + +
50S ASN* 1.3 76.1 + - - +
52S VAL* 1.3 67.4 + - + +
54S ARG* 3.3 61.8 + - - +
55S ASP* 3.8 7.8 + - - +
99S HIS* 5.3 0.7 - - - -
89T ASP* 4.3 5.8 - - - +
91T LYS* 3.7 38.4 - - + +
92T SER* 4.0 21.1 - - - +
95T THR* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S TRP* 4.4 17.0 - - + +
48S GLN* 2.8 28.4 + - + +
49S LEU* 3.6 7.0 - - + +
51S LEU* 1.3 77.1 - - + +
53S LEU* 1.3 59.6 + - + +
55S ASP 3.2 3.5 + - - -
56S ASN* 2.8 45.9 + - + +
59S ILE* 3.6 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q ARG* 4.0 2.1 + - - -
49S LEU* 3.0 42.1 + - + +
52S VAL* 1.3 71.2 - - + +
54S ARG* 1.3 65.4 + - - +
55S ASP 3.2 1.6 - - - -
56S ASN 3.2 16.8 + - - +
57S THR 3.8 6.3 - - - +
58S PHE 4.2 11.9 - - - +
59S ILE* 4.2 7.0 - - + +
99S HIS* 3.6 18.3 + - + +
100S ILE* 3.9 11.9 - - - -
102S ARG* 2.9 28.4 + - - +
103S TRP* 3.7 56.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Q ARG* 3.3 53.0 - - + +
99Q HIS* 4.6 9.9 + - + -
102Q ARG* 3.7 18.0 + - - +
2009Q SO4 3.1 28.1 + - - -
50S ASN 3.1 6.3 + - - +
51S LEU* 3.3 35.3 - - - +
52S VAL 3.2 0.6 - - - -
53S LEU* 1.3 79.6 - - - +
55S ASP* 1.3 90.5 + - - +
99S HIS* 3.6 40.6 - - + +
91T LYS* 3.8 10.3 - - - +
95T THR* 4.6 1.2 - - - +
98T ARG* 3.7 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Q ARG* 4.4 10.2 + - - +
102Q ARG* 3.9 21.7 - - - +
105Q ASP* 4.6 9.0 - - - +
51S LEU* 3.8 6.7 + - - +
52S VAL 3.2 3.0 + - - +
54S ARG* 1.3 124.3 + - - +
56S ASN* 1.3 75.9 + - - +
91T LYS* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q ARG* 4.0 4.9 - - - -
105Q ASP* 4.7 6.9 - - - +
52S VAL* 2.8 35.8 + - + +
53S LEU* 3.2 11.3 - - - +
54S ARG 3.5 0.8 - - - -
55S ASP* 1.3 93.9 - - - +
57S THR* 1.3 63.7 + - - +
58S PHE 3.4 17.7 + - - +
59S ILE 4.9 0.7 - - - +
61S SER* 2.9 29.3 + - - +
102S ARG* 3.1 13.7 + - - -
----------------------------------------------------------
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