Contacts of the helix formed by residues 97 - 111 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47M ASP* 4.6 8.6 + - - -
46N LEU* 4.2 21.9 - - + +
47N ASP* 3.8 22.6 + - - -
50N ASN* 3.2 13.2 - - + +
80N ILE* 4.3 16.4 - - + -
83N LEU* 3.9 28.1 - - + +
93N THR* 3.3 38.6 + - + +
94N TYR 3.6 3.8 - - - +
96N THR* 1.3 100.3 - - + +
98N ARG* 1.3 64.7 + - - +
99N HIS 3.1 0.5 + - - -
100N ILE* 3.2 26.5 + - + -
101N LEU* 3.0 26.7 + - + +
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Residues in contact with ARG 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ARG* 3.8 8.3 - - - +
50N ASN* 3.5 2.8 + - - +
94N TYR* 3.2 16.1 + - - +
95N THR* 3.3 39.2 + - - +
96N THR 3.7 1.4 - - - -
97N TYR* 1.3 75.8 - - - +
99N HIS* 1.3 74.8 + - + +
101N LEU* 3.3 7.6 + - - +
102N ARG* 3.1 25.1 + - - +
2007N SO4 3.0 34.4 + - - -
98O ARG* 5.0 1.6 - - - +
54P ARG* 3.3 61.4 - - + +
55P ASP* 4.5 7.9 + - - +
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Residues in contact with HIS 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N ASN* 3.0 43.1 + - - +
51N LEU* 5.2 0.4 - - - -
53N LEU* 3.6 12.5 - - + +
54N ARG* 3.5 41.4 - - + +
98N ARG* 1.3 92.1 - - + +
100N ILE* 1.3 65.7 + - - +
101N LEU 3.2 0.2 - - - -
102N ARG* 3.3 12.3 + - - +
103N TRP* 3.2 23.4 + - - +
54P ARG* 4.6 10.2 + - + -
99P HIS* 3.8 29.9 + + - -
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Residues in contact with ILE 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N LEU* 3.6 40.4 - - + +
49N LEU* 4.0 21.3 - - + -
50N ASN* 3.2 24.4 - - - +
53N LEU* 3.9 7.6 - - + -
76N ALA* 5.1 1.8 - - + -
80N ILE* 4.1 12.8 - - + -
97N TYR* 3.6 21.1 - - + +
99N HIS* 1.3 77.1 - - - +
101N LEU* 1.3 57.9 + - + +
103N TRP* 3.3 13.1 + - + -
104N ILE* 2.7 51.4 + - + +
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Residues in contact with LEU 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N ILE* 4.4 10.1 - - + -
94N TYR* 3.4 59.7 - - + +
97N TYR* 3.0 21.3 + - + +
98N ARG* 3.6 7.0 - - - +
99N HIS 3.2 0.2 - - - -
100N ILE* 1.3 76.0 - - - +
102N ARG* 1.3 64.0 + - - +
104N ILE* 3.9 3.7 - - + +
105N ASP* 3.0 24.8 + - - +
119N LEU* 3.3 34.8 - - + -
120N GLU 5.5 0.2 - - - +
121N ILE* 3.9 15.9 - - + +
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Residues in contact with ARG 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N LEU* 2.8 39.4 + - - +
56N ASN 2.9 17.6 + - - -
57N THR* 3.1 24.0 + - - +
58N PHE* 5.8 0.6 - - - -
98N ARG 3.1 10.8 + - - +
99N HIS* 3.6 12.2 + - - +
100N ILE 3.3 0.2 - - - -
101N LEU* 1.3 77.4 - - - +
103N TRP* 1.3 69.1 + - - +
105N ASP* 3.4 6.4 - - - +
106N TYR* 3.2 20.3 + - - +
54P ARG 3.8 20.8 + - - +
55P ASP* 3.7 27.7 - - - +
56P ASN* 3.9 4.4 - - - -
57P THR* 3.2 32.7 + - - +
102P ARG* 3.7 33.5 - - - +
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Residues in contact with TRP 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N LEU* 4.0 14.6 - - + -
53N LEU* 3.6 34.5 - - + -
57N THR 4.0 10.5 - - - -
58N PHE* 4.5 7.4 - + - -
59N ILE* 3.4 23.5 - - + +
69N ASP* 2.9 38.7 + - - -
72N VAL* 3.8 12.3 - - + -
73N PHE* 3.4 32.8 - + + -
76N ALA* 4.3 5.2 - - + -
99N HIS 3.2 13.1 + - - +
100N ILE* 3.7 18.4 - - + -
102N ARG* 1.3 86.2 - - - +
104N ILE* 1.3 74.3 + - + +
106N TYR* 3.3 7.5 + - + +
107N MET* 2.9 46.8 + - + +
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Residues in contact with ILE 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N PHE* 4.0 14.4 - - + -
76N ALA 4.4 0.9 - - - +
77N LEU* 3.6 37.2 - - + +
80N ILE* 3.9 24.9 - - + -
100N ILE* 2.7 46.1 + - + +
101N LEU* 3.9 5.4 - - - +
103N TRP* 1.3 81.4 - - + +
105N ASP* 1.3 66.9 + - - +
108N GLN* 2.8 38.7 + - - +
119N LEU* 4.2 18.2 - - + -
121N ILE* 4.3 1.6 - - + -
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Residues in contact with ASP 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N LEU 3.0 13.4 + - - +
102N ARG* 3.4 12.3 - - - +
103N TRP 3.4 0.2 - - - -
104N ILE* 1.3 77.9 - - - +
106N TYR* 1.3 61.8 + - - +
108N GLN* 3.7 8.6 + - - +
109N ASN* 3.0 45.1 + - - +
121N ILE* 3.6 39.0 - - + +
55P ASP 4.5 9.8 - - - +
56P ASN* 4.7 6.9 - - - +
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Residues in contact with TYR 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N PHE* 3.6 36.8 - + + -
65N PRO* 4.1 16.9 - - + +
102N ARG* 3.2 9.7 + - - +
103N TRP* 3.4 11.7 - + + +
104N ILE 3.2 0.2 - - - -
105N ASP* 1.3 79.2 - - - +
107N MET* 1.3 63.2 + - - +
109N ASN* 3.1 7.0 + - - +
110N LEU* 2.7 41.8 + - + +
57P THR* 3.7 26.0 - - + +
58P PHE* 4.1 9.4 - + - -
62P THR 4.1 5.6 - - - -
63P LEU* 2.5 59.8 + - + +
64P TYR* 3.7 15.1 - - - -
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Residues in contact with MET 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N PHE* 5.0 0.4 - - - -
65N PRO* 4.2 14.8 - - + -
69N ASP* 3.8 12.6 - - + +
70N VAL* 3.8 43.7 - - + +
73N PHE* 3.4 27.8 - - + -
103N TRP* 2.9 43.4 + - + +
106N TYR* 1.3 92.2 - - + +
108N GLN* 1.3 57.2 + - - +
110N LEU* 3.5 16.8 - - + +
111N LEU* 3.0 42.0 + - + +
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Residues in contact with GLN 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N PHE* 3.6 16.6 - - + -
77N LEU* 3.6 12.1 - - - +
104N ILE* 2.8 23.0 + - - +
105N ASP* 3.7 11.4 + - - +
107N MET* 1.3 77.5 - - - +
109N ASN* 1.3 63.2 + - - +
112N GLU* 3.5 0.9 + - - -
113N VAL* 3.1 36.5 + - + -
118N LYS* 3.3 31.9 - - + +
119N LEU 2.9 44.9 + - - -
121N ILE* 3.6 19.8 - - - +
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Residues in contact with ASN 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N ASP* 3.0 38.4 + - - +
106N TYR* 3.1 5.7 + - - +
108N GLN* 1.3 78.6 + - - +
110N LEU* 1.3 67.1 + - - +
112N GLU* 3.2 17.5 + - - +
118N LYS* 3.5 23.3 + - - +
61P SER 5.6 3.8 + - - -
63P LEU* 4.1 17.9 - - + +
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Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N ILE* 5.6 2.2 - - + -
65N PRO* 3.8 26.7 - - + -
70N VAL* 5.5 2.0 - - + -
106N TYR* 2.7 29.5 + - + +
107N MET* 3.5 24.0 - - + +
109N ASN* 1.3 75.1 - - - +
111N LEU* 1.3 77.9 + - + +
112N GLU* 3.4 7.4 + - - +
63P LEU* 3.6 23.8 - - + +
64P TYR* 3.5 25.4 - - + +
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Residues in contact with LEU 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N VAL* 4.1 29.4 - - + -
73N PHE* 3.9 32.1 - - + -
107N MET* 3.0 21.6 + - + +
110N LEU* 1.3 93.5 - - + +
112N GLU* 1.3 70.8 + - - +
113N VAL* 3.2 11.4 + - + +
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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