Contacts of the helix formed by residues 169 - 178 (chain B) in PDB entry 4HZF
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 THR 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ILE* 1.3 77.6 - - - +
170B ARG* 1.3 65.4 + - - +
171B GLN* 3.6 13.5 + - - +
172B GLU* 2.9 41.7 + - - +
173B ILE* 3.0 24.5 + - - +
204B ILE* 6.0 0.2 - - - -
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Residues in contact with ARG 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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168B ILE 4.1 3.4 + - - -
169B THR* 1.3 72.6 - - - +
171B GLN* 1.3 62.7 + - - +
173B ILE* 3.4 1.5 + - + -
174B GLY* 3.0 19.1 + - - -
181B ARG* 4.1 17.8 - - + +
184B VAL* 3.7 24.0 - - + +
185B GLY* 4.2 17.2 + - - -
188B LEU* 3.6 30.8 - - + +
199B ALA* 2.8 42.2 + - - +
201B GLY 5.4 2.8 + - - -
202B LYS 6.4 0.6 - - - -
203B THR 5.8 1.2 + - - -
204B ILE* 4.6 12.5 - - - +
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Residues in contact with GLN 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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169B THR* 3.2 12.2 + - - +
170B ARG* 1.3 78.4 - - - +
172B GLU* 1.3 62.8 + - - +
174B GLY* 3.2 2.4 + - - -
175B GLN* 3.0 46.6 + - + +
181B ARG* 3.3 57.1 + - - +
303B GOL 4.7 8.0 + - - -
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Residues in contact with GLU 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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61B ILE* 4.5 1.7 - - + +
64B TYR* 3.2 17.1 + - - +
90B LYS* 2.8 34.9 + - - +
167B LYS 4.5 1.0 - - - +
168B ILE* 3.3 24.8 - - + +
169B THR* 2.9 47.5 + - - +
171B GLN* 1.3 75.3 - - + +
173B ILE* 1.3 66.0 + - - +
175B GLN* 3.2 14.2 + - - +
176B ILE* 2.9 27.9 + - - +
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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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144B ILE* 4.3 21.5 - - + +
147B THR* 4.5 11.7 - - + -
148B LEU* 3.9 21.5 - - + -
151B LEU* 4.9 0.2 - - + -
168B ILE* 3.8 31.0 - - + -
169B THR 3.0 15.1 + - - +
170B ARG 3.8 6.1 - - - +
172B GLU* 1.3 76.3 - - - +
174B GLY* 1.3 59.0 + - - +
176B ILE* 3.1 9.2 + - - +
177B VAL* 2.8 34.2 + - + +
184B VAL* 3.8 28.9 - - + -
188B LEU* 4.2 5.4 - - + -
204B ILE* 4.0 11.9 - - + -
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Residues in contact with GLY 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 ARG 3.0 12.6 + - - -
171B GLN 3.6 3.6 - - - -
173B ILE* 1.3 77.4 - - - +
175B GLN* 1.3 54.1 + - - +
178B GLY* 2.7 30.5 + - - -
179B CYS* 3.0 31.2 + - - +
180B SER 4.5 1.8 - - - -
181B ARG 5.0 0.4 - - - -
184B VAL* 3.5 15.6 - - - +
303B GOL 3.9 2.9 + - - -
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Residues in contact with GLN 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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51B LEU* 4.4 2.4 - - - +
59B GLU* 3.1 50.4 + - - +
60B MET* 3.2 11.3 - - - +
61B ILE* 2.9 48.0 + - + +
88B ARG* 4.7 5.3 + - - +
171B GLN* 3.0 39.3 + - + +
172B GLU* 3.7 10.2 - - - +
174B GLY* 1.3 73.4 - - - +
176B ILE* 1.3 64.5 - - - +
178B GLY* 4.2 1.3 + - - -
303B GOL 3.8 22.3 + - - +
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Residues in contact with ILE 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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60B MET* 2.9 25.6 - - - +
61B ILE* 4.1 22.4 - - + +
64B TYR* 4.0 23.6 - - + +
131B LYS* 4.7 8.5 - - - +
147B THR* 3.9 32.5 - - + +
151B LEU* 5.0 1.8 - - + -
168B ILE* 4.2 16.2 - - + -
172B GLU 2.9 20.4 + - - +
173B ILE* 3.6 7.2 - - - +
175B GLN* 1.3 78.8 - - - +
177B VAL* 1.3 58.8 + - - +
304B GOL 4.1 31.2 - - - +
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Residues in contact with VAL 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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60B MET* 4.1 2.3 - - - +
135B LEU* 4.0 8.1 - - - +
140B VAL* 4.2 12.3 - - + -
143B ARG* 2.6 73.5 + - + +
144B ILE* 3.9 22.2 - - + +
147B THR* 3.1 30.1 - - - +
173B ILE* 2.8 22.3 + - + +
174B GLY 4.3 0.7 - - - +
176B ILE* 1.3 74.6 - - - +
178B GLY* 1.3 55.3 + - - +
179B CYS* 4.2 7.0 - - - -
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Residues in contact with GLY 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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136A ALA* 5.2 10.3 - - - +
137A PHE* 6.1 2.9 - - - -
59B GLU 5.9 1.3 - - - -
60B MET* 4.9 12.6 - - - -
143B ARG* 4.2 8.7 + - - -
174B GLY 2.7 11.7 + - - -
175B GLN* 4.2 4.0 + - - -
176B ILE 3.4 2.0 - - - -
177B VAL* 1.3 80.1 - - - +
179B CYS* 1.3 59.1 + - - +
303B GOL 6.3 0.2 - - - -
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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