Contacts of the helix formed by residues 164 - 176 (chain B) in PDB entry 4HRE
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 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B THR* 1.3 78.2 + - - +
165B GLY* 1.3 70.4 + - - +
167B PHE* 3.4 12.5 - - - +
168B ARG* 3.1 29.7 + - - +
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B SER* 1.3 81.2 - - - +
166B ASP* 1.3 66.2 + - - -
168B ARG* 3.4 11.7 + - - +
169B LYS* 3.4 14.5 + - - +
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Residues in contact with ASP 166 (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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165B GLY* 1.3 71.9 - - - -
167B PHE* 1.3 56.5 + - - +
168B ARG 3.3 0.4 - - - -
169B LYS* 3.5 14.2 - - + +
170B LEU* 2.7 34.0 + - - +
210B VAL* 3.6 39.6 - - + +
211B PRO* 4.5 8.3 - - - +
214B ILE* 3.8 6.7 - - + +
252B LEU* 3.9 18.0 - - + +
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Residues in contact with PHE 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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125B GLU* 3.6 35.4 - - + -
128B LEU* 4.6 4.7 - - + -
129B ILE* 3.8 13.5 - - + -
163B THR* 3.7 31.2 - - + -
164B SER 3.4 9.4 - - - +
166B ASP* 1.3 76.7 - - - +
168B ARG* 1.3 63.7 + - - +
170B LEU* 3.9 1.5 - - + -
171B MET* 3.0 57.5 + - + +
251B ASP* 3.6 41.3 - - + -
252B LEU* 4.0 18.6 - - + +
255B ALA* 3.8 12.8 - - + -
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Residues in contact with ARG 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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160B ILE* 3.6 41.8 + - - +
163B THR* 3.0 46.2 + - - +
164B SER* 3.1 28.8 + - - +
165B GLY 3.6 10.5 + - - +
167B PHE* 1.3 75.1 - - - +
169B LYS* 1.3 70.9 + - + +
170B LEU 3.2 0.2 + - - -
171B MET* 4.9 0.9 - - - -
172B VAL* 2.9 42.3 + - + +
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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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165B GLY 3.4 13.6 + - - +
166B ASP* 3.5 16.8 - - + +
168B ARG* 1.3 83.8 - - + +
170B LEU* 1.3 61.1 + - - +
172B VAL* 4.0 4.6 - - - +
173B ALA* 3.2 23.4 + - - +
211B PRO* 6.4 2.0 - - + -
214B ILE* 3.9 15.6 - - + +
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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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166B ASP 2.7 20.8 + - - +
167B PHE* 3.9 4.5 - - + +
169B LYS* 1.3 72.7 - - - +
171B MET* 1.3 71.1 + - - +
173B ALA* 3.2 2.9 + - - +
174B LEU* 3.2 30.5 + - + +
214B ILE* 3.8 27.1 - - + +
218B THR* 4.0 13.9 - - + -
252B LEU* 4.3 4.5 - - + -
255B ALA* 3.7 31.0 - - + -
256B PHE* 4.0 42.2 - - + +
259B LEU* 4.4 7.6 - - + -
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Residues in contact with MET 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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128B LEU* 3.4 36.1 - - + +
129B ILE* 3.5 20.9 - - + +
132B ILE* 3.5 27.1 - - + +
133B CYS* 4.9 3.4 - - - -
159B ILE* 3.9 25.4 - - + -
163B THR* 4.9 0.2 - - + -
167B PHE* 3.0 53.8 + - + +
170B LEU* 1.3 77.6 - - - +
172B VAL* 1.3 64.8 + - - +
174B LEU* 3.4 5.4 + - - +
175B ALA* 3.0 27.2 + - - +
255B ALA* 4.3 11.0 - - - -
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Residues in contact with VAL 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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156B GLU* 3.5 33.2 - - + +
159B ILE* 4.2 14.6 - - + +
160B ILE* 4.1 18.6 - - + -
168B ARG* 2.9 38.1 + - + +
169B LYS* 4.0 4.7 - - - +
171B MET* 1.3 77.1 - - - +
173B ALA* 1.3 64.7 + - - +
175B ALA* 3.5 10.8 + - - +
176B LYS* 3.5 24.0 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B LYS 3.2 16.1 + - - +
170B LEU 3.2 6.2 + - - +
172B VAL* 1.3 83.7 - - - +
174B LEU* 1.3 62.1 + - - +
176B LYS* 3.4 19.5 - - - +
177B GLY 4.3 0.9 + - - -
178B ARG* 5.2 1.7 + - - +
214B ILE* 4.1 8.7 - - + -
218B THR* 3.7 26.2 - - + +
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Residues in contact with LEU 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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132B ILE* 3.5 24.9 - - + +
133B CYS* 3.8 35.4 - - - -
140B LEU* 3.3 13.5 - - - +
170B LEU* 3.2 29.0 + - + +
171B MET* 4.8 3.6 - - - -
173B ALA* 1.3 79.7 - - - +
175B ALA* 1.3 57.5 + - - +
176B LYS 3.1 0.2 - - - -
177B GLY* 2.9 20.1 + - - -
179B ARG* 3.8 23.1 - - - +
218B THR* 3.4 24.9 - - + +
259B LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 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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132B ILE* 3.8 22.2 - - + -
140B LEU* 3.9 14.2 - - - +
144B ASN* 3.3 28.0 + - - +
155B LEU* 4.5 9.4 - - + -
156B GLU* 6.2 2.5 - - + -
159B ILE* 4.1 14.6 - - + -
171B MET 3.0 18.7 + - - +
172B VAL* 4.1 4.3 - - - +
174B LEU* 1.3 76.7 - - - +
176B LYS* 1.3 59.9 + - - +
177B GLY 3.2 1.0 + - - -
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Residues in contact with LYS 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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140B LEU* 5.1 0.4 - - - -
141B GLN* 3.7 13.2 + - - +
144B ASN* 5.4 2.4 + - - -
156B GLU* 3.5 32.9 + - - +
172B VAL* 3.5 26.4 + - - +
173B ALA* 3.4 15.0 + - - +
174B LEU 3.0 0.4 + - - -
175B ALA* 1.3 78.4 - - - +
177B GLY* 1.3 63.3 + - - +
178B ARG* 3.3 35.3 + - + +
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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