Contacts of the helix formed by residues 114 - 129 (chain B) in PDB entry 2HTH
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 GLY 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ILE* 5.3 1.4 - - - +
21B GLN* 3.9 13.2 - - - +
110B PHE* 4.1 3.2 - - - -
113B HIS* 1.3 79.9 - - - +
115B GLN* 1.3 61.1 + - - +
116B ILE 3.5 2.2 - - - -
117B GLU* 3.8 11.2 + - - +
118B PHE* 3.1 24.9 + - - +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 2.9 34.5 + - - +
79B SER* 4.6 13.5 - - - +
80B ALA* 3.4 35.3 + - - +
82B ILE* 3.5 23.4 - - + +
110B PHE* 3.6 36.6 - - + -
113B HIS 3.3 1.6 - - - -
114B GLY* 1.3 74.5 - - - +
116B ILE* 1.3 82.9 + - - +
118B PHE* 3.1 1.4 + - - +
119B TYR* 2.7 34.7 + - - +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 5.1 4.5 - - - +
114B GLY 3.5 0.6 - - - -
115B GLN* 1.3 95.2 + - - +
117B GLU* 1.3 64.4 + - - +
119B TYR* 3.2 4.9 + - - +
120B ARG* 2.9 25.4 + - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.7 20.2 - - + +
114B GLY* 3.8 11.9 + - - +
115B GLN 3.3 0.6 - - - -
116B ILE* 1.3 80.7 - - - +
118B PHE* 1.3 63.4 + - - +
120B ARG* 3.4 7.7 + - + +
121B ARG* 3.1 40.3 + - + +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.8 29.5 - - + +
21B GLN* 4.1 15.9 - - + -
40B LEU* 3.6 48.9 - - + -
42B LEU* 3.9 25.1 - - + -
47B LEU* 4.1 15.5 - - + -
82B ILE* 4.3 6.5 - - + -
108B LEU* 5.0 1.3 - - + -
110B PHE* 3.8 28.3 - + + -
114B GLY 3.1 16.6 + - - +
115B GLN 3.1 4.6 + - - +
117B GLU* 1.3 75.2 - - - +
119B TYR* 1.3 60.2 + - - +
121B ARG* 3.0 3.0 + - - +
122B LEU* 2.8 38.2 + - + +
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE* 3.5 32.3 + - + +
70B GLU* 3.7 23.5 - - - -
71B GLU* 3.4 44.6 + - + +
82B ILE* 3.8 23.3 - - + +
115B GLN* 2.7 30.0 + - - +
116B ILE* 3.5 5.2 - - - +
118B PHE* 1.3 72.5 - - - +
120B ARG* 1.3 65.5 + - - +
122B LEU* 3.5 2.0 + - - +
123B SER* 2.9 36.4 + - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 2.9 15.0 + - + +
117B GLU* 3.6 11.7 - - + +
118B PHE 3.2 0.2 - - - -
119B TYR* 1.3 79.8 - - - +
121B ARG* 1.3 76.5 + - - +
123B SER* 3.3 6.4 - - - -
124B GLU* 2.9 56.8 + - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.2 19.0 + - + +
19B ILE* 3.7 35.3 - - + +
42B LEU* 3.7 6.3 - - + -
117B GLU* 3.1 31.5 + - + +
118B PHE 3.0 7.2 + - - +
120B ARG* 1.3 88.5 - - - +
122B LEU* 1.3 66.7 + - - +
124B GLU* 2.7 31.4 + - - +
125B GLU* 3.0 28.8 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.6 29.5 - - + +
47B LEU* 4.2 16.6 - - + -
63B LEU* 4.3 11.4 - - + -
66B ILE* 4.7 4.7 - - + -
69B ILE* 3.9 32.8 - - + -
82B ILE* 4.3 16.6 - - + -
84B VAL* 4.8 8.1 - - + -
108B LEU* 5.1 2.5 - - + -
118B PHE* 2.8 26.1 + - + +
119B TYR 3.8 4.5 - - - +
121B ARG* 1.3 76.6 - - - +
123B SER* 1.3 58.3 + - - +
125B GLU* 3.5 1.9 + - + -
126B MET* 2.8 43.4 + - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE* 3.9 16.5 - - - +
119B TYR* 2.9 27.9 + - - -
120B ARG* 3.3 11.9 - - - -
122B LEU* 1.3 77.3 - - - +
124B GLU* 1.3 64.6 + - - +
126B MET* 3.2 6.2 + - - +
127B THR* 2.9 27.1 + - - -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 2.9 44.7 + - + +
121B ARG* 2.7 38.6 + - - +
123B SER* 1.3 75.2 - - - +
125B GLU* 1.3 62.6 + - - +
127B THR* 3.2 7.9 + - - -
128B GLN* 2.8 53.5 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 3.7 16.1 - - + +
42B LEU* 3.8 19.7 - - + -
43B SER 4.1 8.3 - - - +
44B THR* 4.0 9.9 - - - +
63B LEU* 4.1 17.9 - - + -
121B ARG 3.0 20.5 + - - +
122B LEU* 3.9 3.6 - - + +
124B GLU* 1.3 80.3 - - - +
126B MET* 1.3 61.9 + - - +
128B GLN* 4.6 3.6 + - - +
129B ARG* 3.0 20.4 + - - -
130B ARG* 2.6 54.6 + - - +
131B TRP* 3.4 12.3 - - + -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 5.2 11.8 - - - +
63B LEU* 3.8 17.7 - - - +
66B ILE* 3.5 55.9 - - + +
67B VAL 5.5 2.2 - - - +
68B PHE* 6.3 0.9 - - - -
69B ILE* 4.7 13.9 - - + +
122B LEU* 2.8 33.0 + - + +
123B SER* 3.4 10.1 - - - +
125B GLU* 1.3 72.1 - - - +
127B THR* 1.3 61.0 + - - +
129B ARG* 3.4 35.7 + - - +
131B TRP* 4.1 15.0 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 6.2 2.2 - - - -
123B SER* 2.9 19.2 + - - -
124B GLU* 3.6 10.0 - - - -
126B MET* 1.3 72.2 - - - +
128B GLN* 1.3 71.0 + - + +
129B ARG* 3.5 8.8 + - - +
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Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 2.8 43.2 + - - +
125B GLU* 4.4 4.2 + - - +
127B THR* 1.3 80.7 - - + +
129B ARG* 1.3 70.7 + - - +
130B ARG* 3.3 38.6 + - + +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 5.3 3.9 + - - +
47A GLY* 4.9 14.8 - - - +
64B SER* 4.8 9.1 + - - +
66B ILE 5.5 2.8 + - - -
125B GLU 3.0 7.9 + - - -
126B MET* 3.4 35.6 + - - +
127B THR 3.6 7.2 - - - +
128B GLN* 1.3 78.1 - - - +
130B ARG* 1.3 55.4 + - - +
131B TRP* 3.1 66.6 + - + +
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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