Contacts of the helix formed by residues 166 - 177 (chain B) in PDB entry 4HYY
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 ARG 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 4.8 0.4 + - - -
95A ARG* 3.2 49.2 - - - +
117A GLU* 4.1 12.7 + - - -
298A THR* 6.0 0.2 + - - -
137B HIS* 3.0 18.3 + - - +
163B ASN* 2.8 35.3 + - - +
164B THR* 3.8 11.9 - - - +
165B PHE* 1.3 89.1 + - - +
167B PRO* 1.3 68.1 - - - +
168B ASP* 2.9 11.4 + - + +
169B ARG* 3.1 28.4 + - + +
170B LEU* 4.0 0.9 + - - +
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Residues in contact with PRO 167 (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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88A ALA 3.5 19.5 - - - +
91A TYR* 3.6 32.8 - - + -
92A SER* 3.6 28.3 - - - +
95A ARG* 4.3 10.8 - - + -
165B PHE* 3.6 15.8 - - + -
166B ARG* 1.3 81.7 - - - +
168B ASP* 1.3 62.4 + - - +
169B ARG 3.3 0.2 - - - -
170B LEU* 3.1 19.3 + - + +
171B ARG* 3.8 6.3 + - - +
185B LEU* 3.7 20.1 - - + +
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Residues in contact with ASP 168 (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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92A SER* 5.1 3.9 + - - -
96A LYS* 3.9 23.1 + - - +
166B ARG* 2.9 6.5 + - + +
167B PRO* 1.3 81.2 - - - +
169B ARG* 1.3 64.0 + - - +
171B ARG* 3.1 33.0 + - - +
172B ASP* 3.6 10.6 - - - +
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Residues in contact with ARG 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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134B GLN* 3.0 42.0 + - - +
137B HIS* 4.0 17.6 - - + +
166B ARG* 3.1 23.4 + - + +
168B ASP* 1.3 79.9 - - - +
170B LEU* 1.3 61.2 + - - +
171B ARG 3.2 0.7 + - - -
172B ASP* 3.4 21.0 + - - +
173B ILE* 3.6 34.8 + - - +
331B THR 3.7 2.0 + - - -
332B ALA* 2.5 34.6 + - - +
334B GLY 3.9 0.4 - - - +
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Residues in contact with LEU 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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88A ALA* 4.8 0.4 - - + -
137B HIS* 3.2 47.1 - - + +
140B CYS* 3.7 22.7 - - + -
141B VAL* 4.0 10.7 - - + +
165B PHE* 4.2 18.2 - - + -
166B ARG 4.5 2.0 - - - +
167B PRO* 3.1 16.7 + - + +
169B ARG* 1.3 76.9 - - - +
171B ARG* 1.3 58.5 + - - +
173B ILE* 3.3 5.7 + - + +
174B ALA* 2.9 31.6 + - - +
184B VAL* 4.2 11.9 - - + -
185B LEU* 3.5 26.7 - - + -
188B VAL* 4.5 7.0 - - + -
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Residues in contact with ARG 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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92A SER* 5.6 3.1 - - - -
96A LYS* 5.0 14.3 - - - +
167B PRO 4.1 7.2 - - - +
168B ASP* 3.1 27.6 + - - +
170B LEU* 1.3 78.2 - - - +
172B ASP* 1.3 60.3 + - - +
174B ALA* 3.3 8.0 - - - +
175B ASP* 3.0 27.9 + - - +
181B HIS* 3.3 49.5 + - + +
182B ASP* 5.6 4.6 + - - -
185B LEU* 4.0 26.0 - - + +
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Residues in contact with ASP 172 (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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168B ASP* 3.6 13.7 - - - +
169B ARG* 3.7 18.1 + - - +
171B ARG* 1.3 77.1 - - - +
173B ILE* 1.3 60.1 + - - +
175B ASP* 3.0 23.8 + - - +
176B ARG* 3.1 12.0 + - - +
332B ALA* 3.6 30.7 - - + +
333B GLY* 4.6 2.3 - - - -
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Residues in contact with ILE 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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134B GLN* 5.4 0.4 - - - +
137B HIS* 4.3 20.2 - - + +
138B THR* 4.2 24.7 - - + +
141B VAL* 3.7 24.2 - - + -
169B ARG* 3.6 39.9 - - - +
170B LEU* 3.3 7.5 + - - +
172B ASP* 1.3 76.7 - - - +
174B ALA* 1.3 62.4 + - - +
176B ARG* 3.2 3.5 + - - +
177B PHE* 3.0 41.2 + - + -
333B GLY* 3.5 33.9 - - - +
334B GLY* 4.2 1.6 - - - -
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Residues in contact with ALA 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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141B VAL* 4.3 11.8 - - + +
170B LEU 2.9 18.2 + - - +
171B ARG* 3.3 10.3 - - - +
173B ILE* 1.3 77.2 - - - +
175B ASP* 1.3 50.4 + - - +
177B PHE* 3.1 3.5 + - - +
178B ASN 2.8 28.8 + - - -
179B VAL* 3.1 29.8 + - - +
181B HIS* 4.2 9.2 - - - +
184B VAL* 4.2 17.9 - - + -
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Residues in contact with ASP 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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171B ARG 3.0 13.9 + - - +
172B ASP* 3.0 13.5 + - - +
174B ALA* 1.3 70.4 - - - +
176B ARG* 1.3 68.0 + - - +
177B PHE 3.0 1.6 - - - -
178B ASN* 2.9 24.5 + - - +
179B VAL 5.0 0.6 - - - +
181B HIS* 3.1 26.8 + - - -
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Residues in contact with ARG 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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104B GLY* 2.8 31.5 + - - -
138B THR* 4.5 3.4 - - - +
172B ASP 3.1 10.9 + - - +
173B ILE 3.2 7.6 + - - +
175B ASP* 1.3 75.8 - - - +
177B PHE* 1.3 93.2 + - + +
178B ASN* 3.6 6.4 + - - -
331B THR* 4.9 1.5 + - - -
333B GLY* 2.7 46.7 + - - -
334B GLY 3.8 1.4 - - - -
335B ILE 2.6 25.4 + - - +
336B GLY* 3.8 7.9 - - - -
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Residues in contact with PHE 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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102B THR* 6.1 2.0 - - + -
104B GLY* 4.6 5.4 - - - -
138B THR* 4.8 1.1 - - + -
141B VAL* 3.9 16.8 - - + -
142B THR* 3.6 29.4 - - + -
145B LEU* 3.5 33.9 - - + +
173B ILE* 3.0 35.4 + - + +
174B ALA 3.1 4.9 + - - +
176B ARG* 1.3 119.5 - - + +
178B ASN* 1.3 70.7 + - - +
179B VAL* 3.3 8.8 + - + +
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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