Contacts of the helix formed by residues 153 - 164 (chain B) in PDB entry 1HLG
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 SER 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B GLY* 3.5 11.0 - - - -
67B LEU* 3.4 16.7 + - - +
152B HIS* 1.3 84.8 - - - +
154B GLN* 1.3 65.0 + - - -
156B THR* 2.8 34.3 + - - +
157B THR* 3.6 3.2 + - - +
179B LEU 3.0 12.7 + - - -
180B ALA 3.4 14.6 - - - -
182B VAL* 4.4 6.5 + - - +
326B LEU* 4.5 1.6 - - - +
353B HIS* 2.7 33.8 + - - -
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Residues in contact with GLN 154 (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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65B HIS* 5.2 5.1 + - - -
66B GLY 3.8 4.0 + - - -
67B LEU* 3.2 32.4 - - + +
68B LEU 5.3 0.4 - - - +
123B PHE* 3.5 20.7 - - + +
126B MET* 4.1 18.5 - - - +
153B SER* 1.3 82.7 + - - +
155B GLY* 1.3 55.3 + - - +
157B THR* 2.9 24.6 - - + +
158B ILE* 2.9 22.5 + - + +
182B VAL* 4.9 0.8 - - - +
271B ASN* 2.9 31.3 + - - +
275B TRP* 3.2 29.8 + - + +
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Residues in contact with GLY 155 (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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64B GLN* 3.9 16.4 - - - -
65B HIS 3.3 18.4 + - - -
149B TYR* 3.0 22.5 + - - -
151B GLY* 4.2 4.7 - - - -
152B HIS 2.7 21.1 + - - -
154B GLN* 1.3 71.0 - - - +
156B THR* 1.3 59.7 + - - -
158B ILE* 3.4 8.1 + - - +
159B GLY 3.2 8.8 + - - -
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Residues in contact with THR 156 (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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151B GLY* 3.2 29.2 - - - +
152B HIS 3.7 0.2 - - - +
153B SER 2.8 15.0 + - - +
155B GLY* 1.3 75.9 - - - +
157B THR* 1.3 62.9 + - - +
159B GLY 3.1 1.4 + - - -
160B PHE* 2.8 35.2 + - - -
176B PHE* 3.4 21.7 - - - -
178B ALA* 4.0 8.7 - - + -
179B LEU 3.7 20.0 - - - +
181B PRO* 3.3 7.0 - - + +
182B VAL 3.1 21.0 + - - -
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Residues in contact with THR 157 (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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123B PHE* 4.0 22.0 - - - -
153B SER 3.6 3.8 - - - +
154B GLN* 2.9 39.7 + - + +
156B THR* 1.3 73.3 + - - +
158B ILE* 1.3 65.8 + - - +
160B PHE* 3.3 12.3 + - - +
161B ILE* 3.2 25.5 + - - +
182B VAL* 2.8 28.5 - - + +
275B TRP* 3.9 12.4 - - + -
284B PHE* 4.1 11.0 - - - -
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Residues in contact with ILE 158 (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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64B GLN* 4.4 23.8 - - + +
65B HIS 5.7 0.2 - - - +
99B SER* 4.5 2.0 - - - +
123B PHE* 4.4 14.4 - - + +
126B MET* 3.6 38.4 - - + +
127B ALA* 3.5 29.2 - - - +
131B LEU* 3.9 22.4 - - + -
149B TYR* 4.3 3.1 - - - +
154B GLN* 2.9 22.1 + - + +
155B GLY* 3.5 9.6 - - - +
156B THR 3.1 0.2 - - - -
157B THR* 1.3 77.4 - - - +
159B GLY* 1.3 58.3 + - - +
161B ILE* 3.3 4.3 + - - -
162B ALA* 2.9 27.2 + - - +
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Residues in contact with GLY 159 (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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131B LEU* 4.8 0.2 - - - -
149B TYR* 4.3 4.7 - - - -
155B GLY 3.2 6.9 + - - -
156B THR 3.1 7.2 + - - -
158B ILE* 1.3 78.0 - - - +
160B PHE* 1.3 65.5 + - - +
162B ALA* 4.4 2.2 - - - -
163B PHE* 2.8 57.9 + - - +
176B PHE* 3.9 6.3 - - - -
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Residues in contact with PHE 160 (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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156B THR* 2.8 40.6 + - - -
157B THR* 3.6 14.4 - - - +
158B ILE 3.3 0.4 - - - -
159B GLY* 1.3 73.4 - - - +
161B ILE* 1.3 59.7 + - - +
164B SER* 2.9 29.7 + - - -
176B PHE* 3.7 20.6 - + - -
178B ALA* 5.1 0.2 - - + -
181B PRO* 4.1 7.6 - - + -
182B VAL 4.0 16.2 - - - -
183B ALA* 4.0 22.2 - - + -
284B PHE* 3.9 15.0 - - + -
309B VAL* 4.4 14.6 - - + -
312B MET* 3.9 16.8 - - + +
316B ILE* 3.8 18.8 - - + -
335B LEU* 3.9 21.3 - - + -
339B LEU* 4.6 6.5 - - + -
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Residues in contact with ILE 161 (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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123B PHE* 3.7 29.6 - - + +
124B ASP* 4.3 2.7 - - - +
127B ALA* 3.7 20.2 - - + -
128B LYS* 5.5 0.4 - - - +
157B THR 3.2 15.6 + - - +
158B ILE* 3.6 5.4 - - - +
160B PHE* 1.3 73.6 - - - +
162B ALA* 1.3 60.1 + - - +
164B SER* 3.3 4.6 + - - -
165B THR* 2.7 41.5 + - - +
284B PHE* 3.7 17.0 - - + -
307B TYR* 3.2 54.7 - - + +
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Residues in contact with ALA 162 (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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127B ALA* 3.9 19.5 - - + +
131B LEU* 3.8 25.6 - - + -
158B ILE 2.9 20.4 + - - +
159B GLY 3.8 1.8 - - - +
161B ILE* 1.3 74.2 - - - +
163B PHE* 1.3 59.2 + - + +
165B THR* 3.1 4.6 + - - -
166B ASN* 2.8 41.1 + - - +
169B LEU* 3.8 13.5 - - + -
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Residues in contact with PHE 163 (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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131B LEU* 4.1 9.6 - - + -
135B ILE* 5.3 0.7 - - + -
149B TYR* 3.7 42.0 - + + -
159B GLY* 2.8 29.7 + - - +
162B ALA* 1.3 74.5 - - + +
164B SER* 1.3 56.8 + - - +
165B THR 3.4 0.6 + - - -
166B ASN 4.4 1.8 + - - +
167B PRO* 5.3 0.7 - - - +
169B LEU* 3.9 19.1 - - + -
170B ALA* 3.6 25.4 - - + +
173B ILE* 3.5 39.3 - - + -
176B PHE* 3.5 26.9 - + - -
311B ALA 4.3 4.5 - - - +
312B MET* 3.8 20.9 - - + -
313B ASN 4.9 2.3 + - - -
314B VAL* 4.2 14.1 - - + -
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Residues in contact with SER 164 (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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160B PHE 2.9 23.2 + - - -
161B ILE* 3.3 7.6 + - - -
162B ALA 3.2 0.8 - - - -
163B PHE* 1.3 77.8 - - - +
165B THR* 1.3 65.9 + - - +
166B ASN 3.9 0.2 - - - -
167B PRO* 6.0 0.2 - - - -
307B TYR* 5.2 2.6 - - - +
308B ASN* 3.8 28.5 + - - +
309B VAL* 5.4 0.2 - - - -
311B ALA* 3.7 19.8 - - - +
312B MET* 3.8 16.2 - - - -
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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