Contacts of the helix formed by residues 180 - 194 (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 SER 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B GLY* 4.7 0.4 - - - -
179B CYS* 1.3 79.9 - - - +
181B ARG* 1.3 64.1 + - - +
182B GLU* 3.5 17.9 + - - +
183B THR* 2.9 32.7 + - - -
184B VAL* 3.0 23.0 + - - +
186B ARG* 5.0 0.2 + - - -
303B GOL 3.5 13.7 - - - -
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Residues in contact with ARG 181 (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* 4.1 17.2 - - + +
171B GLN* 3.3 65.3 + - - +
174B GLY* 5.0 0.6 - - - -
180B SER* 1.3 72.4 - - - +
182B GLU* 1.3 80.5 + - - +
184B VAL* 3.4 3.3 + - - +
185B GLY* 3.0 22.9 + - - -
303B GOL 3.0 29.4 + - - +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER* 3.5 18.8 - - - +
181B ARG* 1.3 94.8 - - + +
183B THR* 1.3 65.9 + - - +
185B GLY* 3.2 3.1 + - - +
186B ARG* 3.0 40.1 + - + +
303B GOL 4.2 2.4 + - - -
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Residues in contact with THR 183 (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 VAL* 4.3 7.9 - - + -
179B CYS* 4.0 20.4 - - + +
180B SER* 2.9 28.0 + - - -
182B GLU* 1.3 76.3 - - - +
184B VAL* 1.3 63.5 + - - +
186B ARG* 3.0 33.3 + - - +
187B ILE* 3.0 42.9 + - + +
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Residues in contact with VAL 184 (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* 4.2 10.5 - - + +
170B ARG* 3.7 13.5 - - + +
173B ILE* 3.8 28.5 - - + -
174B GLY* 3.5 22.7 - - - +
179B CYS* 3.5 18.6 - - - -
180B SER 3.0 15.6 + - - +
181B ARG 3.6 7.0 - - - +
182B GLU 3.2 0.2 - - - -
183B THR* 1.3 77.9 - - - +
185B GLY* 1.3 56.5 + - - +
187B ILE* 3.1 1.4 + - - +
188B LEU* 2.8 52.1 + - + +
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Residues in contact with GLY 185 (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* 4.2 23.4 + - - -
181B ARG 3.0 14.8 + - - -
182B GLU* 3.2 4.0 + - - -
184B VAL* 1.3 75.8 - - - +
186B ARG* 1.3 62.7 + - - +
188B LEU* 3.5 2.0 + - - +
189B LYS* 3.3 22.2 + - - +
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 3.0 26.4 + - - +
183B THR* 3.0 53.4 + - - +
185B GLY* 1.3 76.3 - - - +
187B ILE* 1.3 67.7 + - + +
189B LYS* 3.3 7.3 + - - +
190B MET* 3.2 19.8 + - - +
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Residues in contact with ILE 187 (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 VAL* 3.8 15.0 - - + -
141B THR* 3.8 39.3 - - + +
144B ILE* 3.7 30.1 - - + -
183B THR* 3.0 39.2 + - + +
184B VAL 4.0 0.2 - - - +
186B ARG* 1.3 79.1 - - + +
188B LEU* 1.3 65.5 + - - +
190B MET* 3.1 13.9 + - + +
191B LEU* 2.9 33.5 + - + +
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Residues in contact with LEU 188 (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* 4.0 15.5 - - + -
148B LEU* 3.8 35.0 - - + -
170B ARG* 3.6 47.1 - - + +
173B ILE* 4.2 2.5 - - + -
184B VAL* 2.8 24.0 + - + +
185B GLY 3.9 4.3 - - - +
186B ARG 3.4 0.2 - - - -
187B ILE* 1.3 77.0 - - - +
189B LYS* 1.3 61.2 + - - +
191B LEU* 3.2 4.5 + - + +
192B GLU* 3.0 23.7 + - - +
197B ILE* 3.8 13.1 - - + +
199B ALA* 4.2 13.4 - - + +
204B ILE* 4.0 16.4 - - + -
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Residues in contact with LYS 189 (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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185B GLY 3.3 11.0 + - - +
186B ARG* 3.6 10.3 - - - +
187B ILE 3.2 0.4 - - - -
188B LEU* 1.3 77.1 - - - +
190B MET* 1.3 63.0 + - - +
192B GLU* 3.3 22.1 + - - +
193B ASP* 2.8 65.5 + - - +
199B ALA* 5.9 0.2 - - - -
305B GOL 5.3 4.6 - - - -
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Residues in contact with MET 190 (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 THR* 3.8 36.3 - - + +
186B ARG 3.2 10.0 + - - +
187B ILE* 3.1 19.9 + - + +
189B LYS* 1.3 81.7 - - - +
191B LEU* 1.3 66.2 + - + +
193B ASP* 3.1 4.5 + - - +
194B GLN* 3.0 42.0 + - - +
305B GOL 3.6 36.8 - - - +
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Residues in contact with LEU 191 (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 THR* 4.3 19.1 - - + +
144B ILE* 4.3 9.4 - - + -
145B ALA* 4.7 17.5 - - + +
148B LEU* 4.0 26.2 - - + -
187B ILE* 2.9 30.3 + - + +
188B LEU* 3.2 8.0 + - + +
190B MET* 1.3 78.3 - - + +
192B GLU* 1.3 58.3 + - - +
194B GLN* 3.4 22.9 + - - +
196B LEU* 3.0 42.6 + - + +
197B ILE* 3.7 17.4 + - + -
302B PO4 5.3 1.8 - - - +
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Residues in contact with GLU 192 (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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188B LEU 3.0 11.5 + - - +
189B LYS* 3.4 27.3 - - - +
191B LEU* 1.3 74.0 - - - +
193B ASP* 1.3 57.9 + - - +
195B ASN* 2.8 26.5 + - - +
197B ILE* 3.3 25.2 - - + +
198B SER* 3.6 2.7 - - - -
199B ALA* 2.9 27.6 + - - +
200B HIS* 2.8 44.3 + - - +
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Residues in contact with ASP 193 (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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189B LYS* 2.8 45.3 + - - +
190B MET 3.1 2.0 + - - +
192B GLU* 1.3 80.0 - - - +
194B GLN* 1.3 58.1 + - - +
195B ASN* 3.3 3.8 + - - +
305B GOL 2.6 47.4 - - - +
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Residues in contact with GLN 194 (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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190B MET* 3.0 36.3 + - - +
191B LEU* 3.4 17.7 + - - +
192B GLU 3.2 0.4 - - - -
193B ASP* 1.3 75.1 - - - +
195B ASN* 1.3 70.7 + - - +
196B LEU* 3.3 31.8 + - + +
305B GOL 4.7 6.5 + - - +
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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