Contacts of the helix formed by residues 168 - 180 (chain B) in PDB entry 1H9T
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 MET 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE* 5.0 7.2 - - + -
164A ILE* 5.5 0.4 - - + -
80B LEU* 4.2 9.6 - - + -
83B LEU* 4.6 11.2 - - + -
101B LEU* 3.6 32.3 - - + -
104B VAL* 3.8 24.7 - - + -
105B ARG* 4.3 12.8 - - - +
108B ILE* 4.8 2.0 - - + -
164B ILE* 2.9 24.0 + - + +
165B LEU* 3.7 38.6 - - + +
166B ASN 3.2 0.4 - - - -
167B GLY* 1.3 80.3 - - - +
169B LYS* 1.3 66.5 + - - +
170B GLY 2.9 3.8 + - - -
171B LEU* 3.1 7.3 + - - +
172B TYR* 2.9 30.9 + - + -
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Residues in contact with LYS 169 (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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76A GLU 5.2 7.8 + - - +
77A THR* 5.9 3.2 - - - +
143B GLU* 4.6 14.0 + - - -
146B TYR* 3.1 54.3 - - + +
150B ARG* 6.1 0.2 - - - +
165B LEU 3.5 4.6 + - - -
166B ASN* 3.6 13.0 - - - +
167B GLY 3.4 1.2 - - - -
168B MET* 1.3 75.1 - - - +
170B GLY* 1.3 70.5 + - - +
172B TYR* 4.4 0.4 - - - -
173B THR* 2.9 31.4 + - + +
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Residues in contact with GLY 170 (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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84B GLU* 4.5 20.7 + - - -
167B GLY 4.9 2.2 + - - -
168B MET 2.9 4.2 + - - -
169B LYS* 1.3 75.6 - - - +
171B LEU* 1.3 59.3 + - - +
173B THR* 2.6 25.7 + - - -
174B ARG* 3.4 12.9 + - - +
177B ARG* 4.1 0.2 + - - -
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Residues in contact with LEU 171 (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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83B LEU* 4.6 24.7 - - + +
84B GLU* 4.2 17.0 - - + +
87B ALA* 4.2 19.7 - - + -
97B LEU* 4.0 24.2 - - + -
98B ILE* 4.7 15.5 - - + -
101B LEU* 3.2 28.5 - - + -
168B MET 3.1 6.9 + - - +
170B GLY* 1.3 71.0 - - - -
172B TYR* 1.3 64.0 + - - +
173B THR 3.0 1.6 + - - -
174B ARG* 3.1 29.1 + - + +
175B ILE* 3.3 16.1 + - + +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.3 14.7 - - + +
102B LEU* 3.7 30.5 - - + -
105B ARG* 2.8 49.9 + - + -
145B ASP* 3.4 29.0 + - - +
146B TYR* 3.7 31.4 - + + +
149B PHE* 4.1 9.7 - + - -
165B LEU* 5.1 4.0 - - + -
168B MET* 2.9 30.1 + - + +
169B LYS* 3.9 4.0 - - - +
171B LEU* 1.3 76.6 - - - +
173B THR* 1.3 59.6 + - - +
175B ILE* 3.9 8.0 - - + +
176B GLY* 3.5 13.2 + - - -
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Residues in contact with THR 173 (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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142B ALA* 4.3 8.9 - - + +
143B GLU* 5.3 7.2 - - - +
146B TYR* 4.5 18.6 - - + -
169B LYS* 2.9 35.4 + - + +
170B GLY* 2.6 21.7 + - - -
172B TYR* 1.3 77.6 - - - +
174B ARG* 1.3 52.7 + - - +
175B ILE 2.9 2.0 - - - -
176B GLY* 2.7 22.5 + - - +
177B ARG* 2.6 53.5 + - - +
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Residues in contact with ARG 174 (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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170B GLY 3.8 10.8 - - - +
171B LEU* 3.1 24.3 + - + +
173B THR* 1.3 77.1 + - - +
175B ILE* 1.3 61.5 + - + +
177B ARG* 3.5 26.8 + - - +
178B HIS* 3.3 38.9 + - + +
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Residues in contact with ILE 175 (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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98B ILE* 3.3 47.6 - - + -
101B LEU* 4.5 14.8 - - + -
102B LEU* 3.3 34.5 - - + -
171B LEU* 3.3 14.6 + - + +
172B TYR* 3.9 11.9 - - + +
173B THR 2.9 0.4 - - - -
174B ARG* 1.3 76.4 - - + +
176B GLY* 1.3 67.0 + - - +
178B HIS* 3.1 4.5 + - - +
179B TYR* 2.8 35.0 + - + +
223B TRP* 4.6 13.6 - - + -
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Residues in contact with GLY 176 (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 ALA* 4.6 0.3 - - - +
142B ALA* 3.7 14.7 - - - +
145B ASP* 5.6 1.8 - - - -
172B TYR 3.5 7.1 + - - -
173B THR* 2.7 14.0 + - - -
175B ILE* 1.3 75.6 - - - +
177B ARG* 1.3 56.0 + - - -
178B HIS 2.8 7.4 + - - -
179B TYR* 4.6 2.2 - - - -
180B PHE* 3.1 48.4 + - - +
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Residues in contact with ARG 177 (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 ALA* 4.4 15.6 - - - +
139B ASP* 4.4 28.4 + - - +
142B ALA* 3.7 13.5 - - + +
143B GLU* 5.9 1.8 - - - +
170B GLY 4.1 0.6 + - - -
173B THR* 2.6 56.3 + - - +
174B ARG* 3.1 38.5 - - - +
175B ILE 3.2 0.2 - - - -
176B GLY* 1.3 70.4 - - - +
178B HIS* 1.3 69.4 + - + +
181B ALA* 5.1 1.4 - - - +
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Residues in contact with HIS 178 (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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174B ARG* 3.3 30.2 + - + +
175B ILE 3.1 5.8 + - - +
176B GLY 3.0 0.6 - - - -
177B ARG* 1.3 88.0 + - + +
179B TYR* 1.3 70.1 + - - +
180B PHE 3.4 1.3 - - - -
181B ALA* 3.3 19.8 - - - +
223B TRP* 4.2 19.7 - + + -
226B MET* 3.7 8.2 - - - +
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Residues in contact with TYR 179 (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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175B ILE* 2.8 24.1 + - + +
176B GLY* 4.2 1.6 - - - +
178B HIS* 1.3 79.9 - - - +
180B PHE* 1.3 94.6 + + - +
181B ALA 3.0 1.4 + - - -
182B ASN 3.5 2.8 + - - -
185B ALA* 3.5 28.3 + - + +
188B LEU* 4.8 0.5 - - - +
189B ALA* 5.8 0.2 - - + -
215B TYR* 4.8 5.8 - - - -
219B SER* 3.1 52.8 + - - -
222B ILE* 3.7 22.6 - - + +
223B TRP* 3.5 41.0 - + + -
226B MET* 3.5 20.0 - - - +
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Residues in contact with PHE 180 (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 ALA* 3.9 14.6 - - + -
141B PHE* 3.4 39.5 - + + -
142B ALA* 3.8 13.2 - - - -
145B ASP* 3.3 49.6 - - + -
176B GLY* 3.1 32.2 + - - +
179B TYR* 1.3 106.6 - + - +
181B ALA* 1.3 66.9 + - - +
182B ASN 2.9 4.9 + - - +
185B ALA* 4.2 1.8 - - - -
186B ARG* 3.3 29.3 + - + +
189B ALA* 3.9 13.7 - - + -
193B TYR* 4.3 1.3 - - - -
215B TYR* 4.8 2.9 - - - -
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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