Contacts of the helix formed by residues 97 - 111 (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 TYR 97 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S LEU* 4.2 18.1 - - + +
47S ASP* 3.8 22.5 + - - -
50S ASN* 3.2 13.5 - - + +
80S ILE* 3.9 21.8 - - + -
83S LEU* 3.5 31.3 - - + +
93S THR* 3.0 38.7 + - + +
94S TYR 3.4 3.6 + - - -
96S THR* 1.3 97.4 - - + +
98S ARG* 1.3 65.0 + - - +
99S HIS 3.2 0.5 + - - -
100S ILE* 3.3 22.9 + - + -
101S LEU* 3.0 27.8 + - + +
47T ASP* 4.5 9.5 + - - -
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Residues in contact with ARG 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q ARG* 3.5 45.7 - - + +
55Q ASP* 3.9 17.5 + - - +
98R ARG* 4.3 6.5 - - - +
50S ASN* 3.4 2.6 + - - +
91S LYS* 4.4 4.0 - - - +
94S TYR* 3.2 13.0 + - - +
95S THR* 3.4 45.5 + - - +
96S THR 3.6 2.0 - - - -
97S TYR* 1.3 76.8 - - - +
99S HIS* 1.3 73.4 - - + +
101S LEU* 3.3 7.3 + - + +
102S ARG* 3.2 24.6 + - - +
2010S SO4 2.6 42.6 + - - -
54T ARG* 4.4 0.8 - - - +
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Residues in contact with HIS 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q ARG* 4.6 9.7 + - + -
99Q HIS* 3.6 31.0 + + - -
102Q ARG* 5.8 1.6 + - - -
50S ASN* 3.0 43.2 - - - +
51S LEU* 5.3 0.2 - - - -
53S LEU* 3.6 22.7 + - + +
54S ARG* 3.6 31.2 - - + +
98S ARG* 1.3 87.8 - - + +
100S ILE* 1.3 67.7 + - - +
102S ARG* 3.4 12.0 + - - +
103S TRP* 3.2 22.5 + - - +
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Residues in contact with ILE 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S LEU* 3.4 42.4 - - + +
49S LEU* 4.1 16.2 - - + -
50S ASN* 3.1 26.9 - - + +
53S LEU* 3.9 7.2 - - + +
76S ALA* 5.1 2.0 - - + -
80S ILE* 3.9 14.4 - - + -
97S TYR* 3.6 25.4 - - + +
99S HIS* 1.3 76.5 - - - +
101S LEU* 1.3 57.2 + - + +
103S TRP* 3.2 13.3 + - + +
104S ILE* 2.7 49.7 + - + +
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Residues in contact with LEU 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S ILE* 3.9 28.0 - - + -
84S VAL* 5.7 1.1 - - + -
94S TYR* 3.7 52.3 - - + +
97S TYR* 3.0 21.0 + - + +
98S ARG* 3.6 8.3 - - + +
99S HIS 3.2 0.2 - - - -
100S ILE* 1.3 74.6 - - + +
102S ARG* 1.3 67.0 + - - +
104S ILE* 3.7 7.2 - - + +
105S ASP* 2.9 25.6 + - - +
119S LEU* 3.9 23.7 - - + +
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Residues in contact with ARG 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q ARG 3.7 17.5 + - - +
55Q ASP* 3.7 25.5 - - - +
56Q ASN 3.9 0.9 - - - -
57Q THR* 3.2 36.1 + - - +
102Q ARG* 3.4 40.2 - - - +
53S LEU* 2.9 38.2 + - - +
56S ASN 3.1 16.8 + - - -
57S THR* 3.1 25.1 + - - +
58S PHE* 5.7 0.6 - - - -
98S ARG 3.2 9.7 + - - +
99S HIS* 3.6 8.8 + - - +
100S ILE 3.4 0.2 - - - -
101S LEU* 1.3 77.2 - - - +
103S TRP* 1.3 66.1 + - - +
105S ASP* 3.4 4.5 + - - +
106S TYR* 3.1 25.0 + - - +
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Residues in contact with TRP 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S LEU* 4.3 7.6 - - + -
53S LEU* 3.7 35.9 - - + -
57S THR 3.9 10.5 - - - -
58S PHE* 4.2 7.9 - + - -
59S ILE* 3.6 18.5 - - + +
69S ASP* 2.8 44.1 + - - -
72S VAL* 3.9 12.1 - - + -
73S PHE* 3.4 36.3 - + + -
76S ALA* 4.1 17.7 - - + -
99S HIS 3.2 12.9 + - - +
100S ILE* 3.2 12.0 + - + -
101S LEU 3.2 0.4 - - - -
102S ARG* 1.3 84.1 - - - +
104S ILE* 1.3 66.4 + - + +
106S TYR* 3.4 6.9 + - + +
107S MET* 2.9 48.4 + - + +
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Residues in contact with ILE 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S PHE* 4.0 16.6 - - + -
76S ALA 4.6 0.9 - - - +
77S LEU* 4.1 17.3 - - + +
80S ILE* 3.9 30.7 - - + -
100S ILE* 2.7 41.3 + - + +
101S LEU* 3.7 10.1 - - + +
103S TRP* 1.3 85.0 - - + +
105S ASP* 1.3 67.5 + - - +
107S MET* 3.1 1.0 + - - +
108S GLN* 2.8 47.1 + - - +
119S LEU* 4.1 20.4 - - + -
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Residues in contact with ASP 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q ASP 4.4 10.3 - - - +
56Q ASN* 4.9 5.2 - - - +
101S LEU 2.9 18.0 + - - +
102S ARG* 3.4 7.6 - - - +
104S ILE* 1.3 77.1 - - - +
106S TYR* 1.3 60.6 + - - +
108S GLN* 3.6 16.5 + - - +
109S ASN* 2.7 39.0 + - - +
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Residues in contact with TYR 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q THR* 3.7 25.1 - - + +
58Q PHE* 4.0 10.8 - + - -
62Q THR 4.4 2.2 - - - -
63Q LEU* 2.4 60.9 + - + +
64Q TYR* 4.3 8.1 - - - -
58S PHE* 3.6 41.3 - + + -
65S PRO* 4.1 19.6 - - + +
102S ARG* 3.1 13.7 + - - +
103S TRP* 3.4 10.3 - - - +
104S ILE 3.2 0.2 - - - -
105S ASP* 1.3 75.0 - - - +
107S MET* 1.3 69.4 + - + +
109S ASN 3.2 2.6 + - - -
110S LEU* 2.9 38.0 + - + +
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Residues in contact with MET 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S PHE* 4.8 0.9 - - - -
65S PRO* 4.0 23.1 - - + -
69S ASP* 3.8 35.9 - - + +
70S VAL* 3.9 19.3 - - + -
73S PHE* 3.6 24.4 - - + -
103S TRP* 2.9 44.3 + - + +
106S TYR* 1.3 89.1 - - + +
108S GLN* 1.3 59.0 + - - +
110S LEU* 3.7 8.5 - - + +
111S LEU* 3.0 46.7 + - + +
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Residues in contact with GLN 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S PHE* 3.9 10.8 - - + -
77S LEU* 4.0 5.2 - - - +
104S ILE* 2.8 35.7 + - - +
105S ASP* 3.6 19.3 + - - +
107S MET* 1.3 77.7 - - - +
109S ASN* 1.3 66.7 + - - +
112S GLU* 3.1 4.3 + - - -
113S VAL* 3.0 46.4 + - + +
118S LYS* 3.4 26.2 - - + +
119S LEU* 2.9 43.9 + - - +
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Residues in contact with ASN 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU* 3.9 22.6 - - + +
105S ASP* 2.7 35.5 - - - +
106S TYR 3.2 3.6 + - - +
108S GLN* 1.3 79.9 + - - +
110S LEU* 1.3 66.8 + - - +
112S GLU* 3.0 20.0 + - - +
118S LYS* 4.8 16.2 + - - +
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Residues in contact with LEU 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU* 3.7 17.5 - - + +
64Q TYR* 5.7 3.4 - - + +
9S LYS* 5.2 1.2 - - - +
10S PHE* 4.5 9.9 - - + -
13S LEU* 4.0 28.4 - - + +
15S ILE* 4.5 14.6 - - + -
65S PRO* 3.6 30.7 - - + -
106S TYR* 2.9 37.8 + - + +
107S MET* 3.7 12.6 - - + +
109S ASN* 1.3 78.3 - - - +
111S LEU* 1.3 76.0 + - + +
112S GLU* 3.4 9.5 + - - +
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Residues in contact with LEU 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S LEU* 4.0 25.7 - - + +
9S LYS* 4.0 22.0 - - + +
10S PHE* 3.9 36.3 - - + +
13S LEU* 4.6 1.8 - - + -
70S VAL* 3.9 26.5 - - + -
73S PHE* 4.1 15.5 - - + -
107S MET* 3.0 36.3 + - + +
110S LEU* 1.3 94.4 - - + +
112S GLU* 1.3 72.8 + - - +
113S VAL* 3.0 7.3 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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