Contacts of the helix formed by residues 97 - 111 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47I ASP* 4.5 8.6 + - - -
46J LEU* 4.3 17.3 - - + +
47J ASP* 3.8 22.5 + - - -
50J ASN* 3.3 10.3 - - + +
80J ILE* 4.0 15.5 - - + -
83J LEU* 3.9 32.0 - - + +
93J THR* 3.2 39.8 + - + +
94J TYR 3.6 3.1 - - - -
96J THR* 1.3 101.4 - - + +
98J ARG* 1.3 63.9 + - - +
99J HIS 3.1 3.6 + - - -
100J ILE* 3.4 26.4 + - + -
101J LEU* 2.9 29.9 + - + +
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Residues in contact with ARG 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ARG* 3.9 9.7 - - - +
50J ASN* 3.5 2.4 + - - +
91J LYS* 4.3 1.0 - - - +
94J TYR* 3.2 15.0 + - + +
95J THR* 3.4 41.2 + - - +
96J THR 3.6 1.6 - - - -
97J TYR* 1.3 77.6 - - - +
99J HIS* 1.3 77.5 + - + +
101J LEU* 3.3 7.6 + - + +
102J ARG* 3.1 23.7 + - - +
2006J SO4 2.8 42.0 + - - -
98K ARG* 4.1 6.5 - - - +
54L ARG* 3.3 53.2 - - + +
55L ASP* 4.1 8.3 - - - +
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Residues in contact with HIS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J ASN* 2.9 42.9 + - - +
51J LEU* 5.2 0.7 - - - -
53J LEU* 3.6 23.1 + - - +
54J ARG* 3.5 31.7 + - + +
98J ARG* 1.3 90.5 - - + +
100J ILE* 1.3 67.3 + - - +
101J LEU 3.1 0.9 - - - -
102J ARG* 3.1 11.9 + - - +
103J TRP* 3.0 23.4 + - - +
54L ARG* 4.5 10.5 + - + -
99L HIS* 3.7 31.2 + + - -
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Residues in contact with ILE 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J LEU* 3.4 35.9 - - + +
49J LEU* 4.0 20.0 - - + -
50J ASN* 3.1 24.2 - - + +
53J LEU* 3.9 9.3 - - + +
76J ALA* 5.2 1.6 - - + -
80J ILE* 3.8 14.6 - - + -
97J TYR* 3.6 29.2 - - + +
99J HIS* 1.3 74.8 - - - +
101J LEU* 1.4 51.5 + - + +
103J TRP* 3.2 12.5 + - + +
104J ILE* 2.8 55.1 + - + +
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ILE* 3.8 18.4 - - + -
84J VAL* 5.4 0.7 - - + -
93J THR* 5.0 0.9 - - + +
94J TYR* 3.5 53.4 - - + +
97J TYR* 2.9 21.3 + - + +
98J ARG* 3.6 7.4 - - + +
99J HIS 3.1 0.2 - - - -
100J ILE* 1.4 75.7 - - - +
102J ARG* 1.3 64.3 + - - +
104J ILE* 3.3 5.4 + - + +
105J ASP* 2.9 25.8 + - - +
119J LEU* 3.6 31.6 - - + -
121J ILE* 4.0 19.5 - - + +
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Residues in contact with ARG 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J LEU* 2.8 38.8 + - - +
56J ASN 2.8 19.0 + - - -
57J THR* 3.1 21.8 + - - +
58J PHE* 5.8 0.4 - - - -
98J ARG 3.1 8.7 + - - +
99J HIS* 3.1 13.1 + - - +
101J LEU* 1.3 76.7 - - - +
103J TRP* 1.3 64.2 + - - +
105J ASP* 3.5 4.9 + - - +
106J TYR* 3.1 24.8 + - - +
53L LEU 4.1 0.7 - - - -
54L ARG 3.7 25.3 + - - +
55L ASP* 3.8 23.4 - - - +
56L ASN 4.0 1.1 - - - -
57L THR* 2.9 46.8 + - - +
102L ARG* 3.8 24.9 - - - +
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Residues in contact with TRP 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J LEU* 4.3 7.9 - - + -
53J LEU* 3.6 39.1 - - + +
57J THR 4.0 10.3 - - - -
58J PHE* 4.5 7.0 - + - -
59J ILE* 4.9 4.9 - - + -
69J ASP* 2.9 50.0 + - + +
72J VAL* 4.0 15.9 - - + -
73J PHE* 3.5 35.7 - + + -
76J ALA* 4.3 11.9 - - + -
99J HIS 3.0 15.2 + - - +
100J ILE* 3.8 10.1 - - + -
102J ARG* 1.3 83.8 - - - +
104J ILE* 1.3 83.0 + - + +
106J TYR* 3.2 7.8 + - + +
107J MET* 2.8 43.5 + - + +
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Residues in contact with ILE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J PHE* 3.9 15.0 - - + -
76J ALA 4.5 1.3 - - - +
77J LEU* 4.0 26.9 - - + +
80J ILE* 3.8 28.9 - - + -
100J ILE* 2.8 40.9 + - + +
101J LEU* 3.7 7.6 - - + +
103J TRP* 1.3 84.2 - - + +
105J ASP* 1.3 68.5 + - - +
108J GLN* 2.9 50.5 + - - +
119J LEU* 4.2 9.2 - - + -
121J ILE* 4.5 5.2 - - + -
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Residues in contact with ASP 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU 2.9 17.8 + - - +
102J ARG* 3.6 7.2 - - - +
104J ILE* 1.3 75.9 - - - +
106J TYR* 1.3 63.3 + - - +
108J GLN* 3.7 15.9 + - - +
109J ASN* 2.9 39.7 + - - +
121J ILE* 4.3 17.5 - - + +
55L ASP 4.7 9.4 - - - +
56L ASN* 5.1 5.7 - - - +
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Residues in contact with TYR 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J PHE* 3.4 40.8 - + - -
65J PRO* 3.8 23.3 - - + +
102J ARG* 3.1 14.0 + - - +
103J TRP* 3.3 12.6 - + + +
105J ASP* 1.3 76.6 - - - +
107J MET* 1.3 70.2 + - - +
109J ASN 3.2 2.6 + - - -
110J LEU* 2.9 36.6 + - + +
57L THR* 3.7 25.6 - - + +
58L PHE* 4.2 6.3 - + - -
62L THR 4.0 6.3 - - - -
63L LEU* 2.5 56.5 + - + +
64L TYR* 4.1 7.6 - - - -
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Residues in contact with MET 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J PHE* 5.1 0.9 - - - -
65J PRO* 4.2 10.8 - - + -
69J ASP* 3.7 28.0 - - + +
70J VAL* 3.7 35.7 - - + +
73J PHE* 3.5 26.5 - - + -
103J TRP* 2.8 42.4 + - + +
104J ILE 3.3 0.2 + - - -
106J TYR* 1.3 89.2 - - + +
108J GLN* 1.3 58.0 + - - +
110J LEU* 4.1 16.2 - - + -
111J LEU* 3.0 40.1 + - + +
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Residues in contact with GLN 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J PHE* 3.7 12.3 - - + -
77J LEU* 4.0 3.8 - - - +
104J ILE* 2.9 36.7 + - - +
105J ASP* 3.7 23.2 + - - +
107J MET* 1.3 78.2 - - - +
109J ASN* 1.3 61.8 + - - +
112J GLU* 3.2 3.5 + - - -
113J VAL* 3.0 40.2 + - + -
118J LYS* 3.4 33.6 - - + +
119J LEU 2.7 45.2 + - - -
121J ILE* 4.3 3.4 - - - +
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Residues in contact with ASN 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J ASP* 2.9 34.2 + - - +
106J TYR 3.2 3.7 + - - +
108J GLN* 1.3 77.8 + - - +
110J LEU* 1.3 66.0 + - - +
111J LEU 3.2 2.1 + - - -
112J GLU* 3.3 18.3 + - - +
118J LYS* 3.4 24.7 - - - +
63L LEU* 4.1 20.8 - - + +
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ILE* 5.8 2.0 - - + -
65J PRO* 3.6 38.8 - - + -
70J VAL* 5.2 2.5 - - + -
106J TYR* 2.9 28.4 + - + +
107J MET* 3.3 20.4 + - + +
109J ASN* 1.3 77.4 - - - +
111J LEU* 1.3 79.6 + - + +
112J GLU* 3.6 4.3 + - - +
63L LEU* 3.7 20.2 - - + +
64L TYR* 3.7 23.6 - - - +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J VAL* 4.0 32.1 - - + -
73J PHE* 4.1 16.6 - - + -
107J MET* 3.0 32.5 + - + +
110J LEU* 1.3 95.8 - - + +
112J GLU* 1.3 70.8 + - - +
113J VAL* 3.4 10.0 + - + +
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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