Contacts of the helix formed by residues 97 - 111 (chain T) 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 TYR 97 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47S ASP* 4.7 7.6 + - - -
46T LEU* 3.9 23.2 - - + +
47T ASP* 3.8 22.1 + - - -
50T ASN* 3.3 9.4 - - + +
80T ILE* 5.4 11.4 - - + -
83T LEU* 4.0 29.1 - - + +
93T THR* 3.3 38.2 + - + +
94T TYR 3.6 4.0 - - - +
95T THR 3.3 0.2 - - - -
96T THR* 1.3 99.6 - - + +
98T ARG* 1.3 62.8 + - - +
99T HIS 3.1 3.7 + - - -
100T ILE* 3.3 27.6 + - + -
101T LEU* 2.9 28.4 + - + +
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Residues in contact with ARG 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Q ARG* 3.8 5.5 - - - +
2009Q SO4 2.6 40.4 + - - -
54R ARG* 3.5 52.0 - - + +
55R ASP* 4.4 8.2 - - - +
54S ARG* 3.7 8.5 - - - +
50T ASN* 3.6 2.2 + - - +
94T TYR 3.2 16.3 + - - +
95T THR* 3.2 41.6 + - - +
96T THR 3.7 1.0 - - - -
97T TYR* 1.3 77.8 - - - +
99T HIS* 1.3 75.7 + - + +
101T LEU* 3.6 7.5 + - - +
102T ARG* 3.1 24.1 + - - +
123T HIS 4.8 7.2 + - - +
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Residues in contact with HIS 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R ARG* 4.5 10.5 + - + -
99R HIS* 3.7 31.2 + + - -
50T ASN* 3.0 46.8 + - - +
51T LEU* 5.3 0.7 - - - -
53T LEU* 3.6 12.0 + - + +
54T ARG* 3.5 40.1 - - + +
98T ARG* 1.3 92.3 - - + +
100T ILE* 1.3 67.3 + - - +
102T ARG* 3.2 11.8 + - - +
103T TRP* 3.1 22.5 + - - +
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Residues in contact with ILE 100 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T LEU* 3.5 44.6 - - + +
49T LEU* 4.0 15.0 - - + -
50T ASN* 3.1 22.6 - - + +
53T LEU* 4.0 8.0 - - - +
80T ILE* 4.1 15.3 - - + -
97T TYR* 3.6 25.6 - - + +
99T HIS* 1.3 76.6 - - - +
101T LEU* 1.3 57.0 + - - +
103T TRP* 3.2 13.5 + - + +
104T ILE* 2.7 51.3 + - + +
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Residues in contact with LEU 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T ILE* 3.9 14.6 - - + -
84T VAL* 5.5 0.2 - - + -
94T TYR* 3.5 49.8 - - + +
97T TYR* 2.9 25.4 + - + +
98T ARG* 3.7 6.5 - - - +
100T ILE* 1.3 73.7 - - - +
102T ARG* 1.3 65.7 + - - +
104T ILE* 3.8 4.2 - - + +
105T ASP* 2.9 24.8 + - - +
119T LEU* 3.1 35.7 - - + -
121T ILE* 3.8 16.4 - - + +
123T HIS* 4.8 12.8 - - + +
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Residues in contact with ARG 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R LEU 4.1 1.1 - - - -
54R ARG 3.9 17.2 + - - +
55R ASP* 3.8 19.6 - - - +
56R ASN 3.9 4.9 - - - -
57R THR* 3.0 49.1 + - - +
102R ARG* 3.9 21.4 - - - +
53T LEU* 3.0 38.8 + - - +
56T ASN 3.0 17.0 + - - -
57T THR* 3.1 24.4 + - - +
58T PHE* 5.4 0.6 - - - -
98T ARG 3.1 14.7 + - - +
99T HIS* 3.2 10.0 + - - +
101T LEU* 1.3 75.2 - - - +
103T TRP* 1.3 70.7 + - - +
105T ASP* 3.4 5.5 - - - +
106T TYR* 3.1 24.9 + - - +
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Residues in contact with TRP 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T LEU* 4.2 9.2 - - + -
53T LEU* 3.6 31.9 - - + -
57T THR 4.0 10.1 - - - -
58T PHE* 4.3 7.4 - + - -
59T ILE* 3.5 18.0 - - + +
69T ASP* 3.0 42.4 + - - -
72T VAL* 3.9 12.3 - - + -
73T PHE* 3.4 31.4 - + + -
76T ALA* 4.1 18.4 - - + -
99T HIS 3.1 9.9 + - - +
100T ILE* 3.6 18.6 - - + +
102T ARG* 1.3 91.6 - - - +
104T ILE* 1.3 73.5 + - + +
106T TYR* 3.2 5.1 + - + +
107T MET* 2.9 48.7 + - + +
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Residues in contact with ILE 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T PHE* 4.1 15.5 - - + -
76T ALA 4.3 4.9 - - - +
77T LEU* 4.0 18.4 - - + -
80T ILE* 3.9 34.1 - - + -
100T ILE* 2.7 44.7 + - + +
101T LEU* 3.8 6.1 - - + +
103T TRP* 1.3 79.6 - - + +
105T ASP* 1.3 69.3 + - - +
108T GLN* 2.9 49.6 + - - +
119T LEU* 4.1 14.6 - - + -
121T ILE* 4.8 1.1 - - + -
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Residues in contact with ASP 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R ASP 4.5 8.9 - - - +
56R ASN* 4.8 6.2 - - - +
101T LEU 2.9 17.7 + - - +
102T ARG* 3.4 8.3 - - - +
104T ILE* 1.3 77.8 - - - +
106T TYR* 1.3 64.1 + - - +
108T GLN* 3.7 9.9 + - - +
109T ASN* 3.3 32.7 + - - +
121T ILE* 3.7 34.8 - - + +
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Residues in contact with TYR 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57R THR* 3.7 25.4 - - + +
58R PHE* 4.2 8.2 - + - -
62R THR 4.4 2.5 - - - -
63R LEU* 2.5 64.6 + - + +
64R TYR* 4.3 5.7 - - - -
58T PHE* 3.6 39.9 - + + -
64T TYR* 5.6 1.7 - - - -
65T PRO* 3.8 18.2 - - + +
102T ARG* 3.1 14.1 + - - +
103T TRP* 3.4 11.0 - + + +
104T ILE 3.1 0.6 - - - -
105T ASP* 1.3 79.6 - - - +
107T MET* 1.3 66.3 + - - +
110T LEU* 2.9 42.6 + - + +
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Residues in contact with MET 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T PHE* 4.9 0.9 - - - -
65T PRO* 4.1 18.4 - - + -
69T ASP* 3.9 34.5 - - + +
70T VAL* 4.0 10.1 - - + -
73T PHE* 3.4 24.5 - - + -
103T TRP* 2.9 45.5 + - + +
106T TYR* 1.3 88.8 - - + +
108T GLN* 1.3 58.2 + - - +
110T LEU* 4.2 9.6 - - + -
111T LEU* 2.9 57.8 + - + +
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Residues in contact with GLN 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T PHE* 3.5 19.0 - - + -
77T LEU* 3.7 10.9 - - - +
104T ILE* 2.9 31.3 + - - +
105T ASP* 3.7 6.5 + - - +
107T MET* 1.3 73.7 - - - +
109T ASN* 1.3 70.2 + - - +
112T GLU 3.2 2.4 + - - -
113T VAL* 3.0 42.5 + - + +
118T LYS* 3.3 25.9 - - + +
119T LEU* 2.8 46.1 + - - +
121T ILE* 4.0 15.4 - - - +
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Residues in contact with ASN 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R LEU* 4.0 20.0 - - + +
105T ASP* 3.3 26.7 + - - +
106T TYR 3.4 3.2 + - - +
107T MET 3.2 0.2 - - - -
108T GLN* 1.3 86.7 + - - +
110T LEU* 1.3 66.4 + - - +
111T LEU 3.1 0.9 - - - -
112T GLU* 3.2 16.2 + - - +
118T LYS* 3.7 22.8 + - - +
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Residues in contact with LEU 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R LEU* 3.8 15.4 - - + +
64R TYR* 3.6 25.8 - - + +
9T LYS* 4.1 12.0 - - - -
10T PHE* 4.7 2.9 - - + -
13T LEU* 3.7 29.2 - - + +
15T ILE* 3.9 13.7 - - + -
65T PRO* 3.5 32.8 - - + -
106T TYR* 2.9 35.0 + - + +
107T MET* 3.6 13.2 - - + +
109T ASN* 1.3 77.5 - - - +
111T LEU* 1.3 71.1 + - + +
112T GLU* 3.5 3.3 + - - +
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Residues in contact with LEU 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T LEU* 4.1 26.0 - - + +
9T LYS* 3.6 21.3 - - + +
10T PHE* 3.9 38.4 - - + +
13T LEU* 4.3 2.5 - - + -
70T VAL* 4.3 17.0 - - + -
73T PHE* 4.0 21.3 - - + -
107T MET* 2.9 36.8 + - + +
110T LEU* 1.3 95.7 - - + +
112T GLU* 1.3 70.0 + - - +
113T VAL* 3.1 6.8 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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