Contacts of the helix formed by residues 139 - 153 (chain B) in PDB entry 2H1H
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 HIS 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B HIS* 3.9 21.9 + + - -
138B GLN* 1.3 75.1 - - - +
140B ALA* 1.3 73.2 + - + +
141B VAL* 2.8 47.1 + - + +
142B GLU* 2.8 22.8 + - + +
143B ARG* 3.0 9.9 + - - +
266B HIS* 6.2 0.2 - - - -
290B TYR* 3.5 42.1 + + + +
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Residues in contact with ALA 140 (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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13B ASP* 5.3 5.6 - - - +
16B HIS* 4.0 27.1 - - + +
138B GLN 3.5 2.4 + - - -
139B HIS* 1.3 77.0 + - + +
141B VAL* 1.3 63.3 + - - +
143B ARG* 3.3 13.7 + - - +
144B THR* 3.0 29.9 + - - +
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Residues in contact with VAL 141 (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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16B HIS* 3.5 36.6 - - + +
19B PRO* 3.8 24.0 - - + -
139B HIS* 2.8 29.4 + - + +
140B ALA* 1.3 77.6 - - - +
142B GLU* 1.3 59.2 + - - +
144B THR* 3.5 2.9 + - - -
145B ARG* 3.0 34.2 + - - +
163B TYR* 3.8 13.2 - - + +
290B TYR* 3.8 31.9 - - + -
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Residues in contact with GLU 142 (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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138B GLN* 4.1 22.2 - - + +
139B HIS* 2.8 20.5 + - + +
141B VAL* 1.3 70.9 - - - +
143B ARG* 1.3 64.0 + - - +
145B ARG* 3.3 23.3 + - - +
146B GLU* 3.0 24.3 + - - +
156B LYS* 3.1 29.8 + - - +
159B THR 5.1 0.3 - - - +
160B GLN* 4.7 2.4 + - - -
290B TYR* 2.7 38.3 + - + -
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Residues in contact with ARG 143 (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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114B MET* 3.6 31.8 - - + +
118B THR* 3.0 26.7 + - - -
120B ARG* 5.6 3.8 - - - +
134B ILE* 2.8 44.5 + - + +
135B ALA 2.9 23.4 + - - +
136B LYS* 3.5 28.4 - - - +
138B GLN* 3.7 18.6 - - + +
139B HIS 3.0 12.4 + - - +
140B ALA* 3.3 12.3 + - - +
142B GLU* 1.3 75.6 - - - +
144B THR* 1.3 58.5 + - - +
146B GLU 3.3 1.4 + - - -
147B LEU* 3.0 26.0 + - - +
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Residues in contact with THR 144 (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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7B LYS* 5.3 3.5 + - - -
16B HIS* 4.3 8.7 + - - +
17B THR* 3.7 31.4 + - + -
20B ALA* 3.6 17.9 - - + -
93B ALA* 4.3 14.7 + - + +
114B MET* 6.0 2.6 - - - +
140B ALA* 3.0 19.0 + - - +
141B VAL 3.8 4.3 - - - -
143B ARG* 1.3 74.6 - - - +
145B ARG* 1.3 64.7 + - - +
147B LEU* 3.2 8.0 + - - +
148B PHE* 2.9 39.0 + - + -
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Residues in contact with ARG 145 (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 PRO* 4.3 5.8 + - + -
20B ALA* 3.8 23.3 - - - +
23B ASP* 2.5 44.0 + - - +
141B VAL* 3.0 26.7 + - - +
142B GLU* 3.3 32.9 + - - +
144B THR* 1.3 75.2 - - - +
146B GLU* 1.3 58.3 + - - +
148B PHE* 3.2 2.3 + - - +
149B ALA* 2.9 30.3 + - - +
154B TYR* 4.4 2.4 + - - -
156B LYS* 3.6 16.0 - - + +
157B PRO* 3.6 22.4 + - - +
159B THR* 3.1 31.5 + - - -
160B GLN 4.4 0.4 + - - -
161B GLY* 3.2 23.7 - - - +
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Residues in contact with GLU 146 (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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133B HIS 3.6 5.7 - - - +
134B ILE* 4.1 11.7 - - + -
135B ALA* 4.4 3.3 + - - +
138B GLN* 3.1 33.8 + - - +
142B GLU 3.0 12.2 + - - +
143B ARG 3.5 8.3 - - - +
145B ARG* 1.3 73.5 - - - +
147B LEU* 1.3 60.8 + - - +
149B ALA* 3.3 4.2 + - + +
150B LYS* 2.7 74.0 + - + +
156B LYS* 3.8 17.7 - - + +
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Residues in contact with LEU 147 (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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91B ILE* 3.9 17.5 - - + -
92B ASP 3.6 24.0 - - - +
93B ALA* 3.8 19.1 - - + -
113B GLY* 4.2 14.6 - - - +
114B MET* 4.3 13.9 - - + -
132B HIS* 3.9 26.7 - - + -
134B ILE* 3.7 15.8 - - + +
143B ARG 3.0 14.5 + - - +
144B THR* 3.2 9.8 + - - +
146B GLU* 1.3 77.8 - - - +
148B PHE* 1.3 54.9 + - + +
150B LYS* 3.8 1.5 - - - +
151B SER* 2.6 45.3 + - - +
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Residues in contact with PHE 148 (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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5B ILE* 3.6 37.7 - - + -
17B THR* 4.0 12.8 - - + -
20B ALA* 3.4 22.7 - - + -
21B LEU* 3.9 11.4 - - + -
24B ALA* 4.5 0.2 - - + -
33B PHE* 3.8 24.9 - + - -
91B ILE* 3.6 30.5 - - + -
93B ALA* 4.5 5.8 - - + -
144B THR* 2.9 35.0 + - + +
145B ARG* 3.6 3.4 - - - +
147B LEU* 1.3 76.5 - - + +
149B ALA* 1.3 59.4 + - - +
151B SER* 4.4 3.6 - - - -
152B LEU* 2.8 41.9 + - + +
154B TYR* 3.5 13.5 - - - +
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Residues in contact with ALA 149 (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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145B ARG 2.9 17.4 + - - +
146B GLU* 3.7 4.9 - - + +
148B PHE* 1.3 75.1 - - - +
150B LYS* 1.3 60.2 + - + +
153B GLY* 2.9 27.5 + - - -
154B TYR* 3.0 50.1 + - + +
156B LYS* 3.7 19.7 - - + +
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Residues in contact with LYS 150 (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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112B HIS* 4.9 0.5 - - - -
132B HIS* 3.4 33.8 - - + +
133B HIS* 2.7 23.1 + - - +
134B ILE* 4.0 12.1 - - + -
146B GLU* 2.7 52.7 + - + +
147B LEU 4.0 2.5 - - - +
149B ALA* 1.3 79.2 - - + +
151B SER* 1.3 60.7 + - - +
153B GLY* 4.1 4.7 + - - -
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Residues in contact with SER 151 (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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89B ALA* 5.1 0.7 - - - +
91B ILE* 3.9 17.1 - - - +
112B HIS* 3.2 59.0 + - - +
130B ARG* 5.1 0.9 + - - -
132B HIS* 3.4 8.0 + - - -
147B LEU* 2.6 30.4 + - - +
148B PHE 3.8 3.1 - - - -
150B LYS* 1.3 77.0 - - - +
152B LEU* 1.3 65.7 + - - +
153B GLY 3.5 0.2 - - - -
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Residues in contact with LEU 152 (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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1B MET* 4.2 17.1 - - - +
3B VAL* 3.8 24.2 - - + -
24B ALA* 4.0 9.0 - - + -
28B ILE* 3.9 18.1 - - + +
31B ILE* 4.0 19.1 - - + -
33B PHE* 4.2 6.1 - - + -
89B ALA* 4.2 10.5 - - + -
91B ILE* 4.1 21.1 - - + -
148B PHE* 2.8 22.3 + - + +
151B SER* 1.3 83.0 - - - +
153B GLY* 1.3 61.9 - - - +
154B TYR* 3.6 21.3 - - + -
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Residues in contact with GLY 153 (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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28B ILE* 5.9 0.2 - - - -
149B ALA 2.9 8.8 + - - -
150B LYS 4.1 4.3 + - - -
151B SER 3.5 2.6 - - - -
152B LEU* 1.3 80.3 - - - +
154B TYR* 1.3 57.9 + - - +
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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