Contacts of the helix formed by residues 221 - 229 (chain B) in PDB entry 4ZM9
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 HIS 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PRO 5.1 5.3 + - - -
189B ILE* 4.2 23.4 - - + +
220B GLY* 1.3 69.3 - - - -
222B GLY* 1.3 64.3 + - - +
223B GLU* 3.3 35.7 + - + -
224B SER* 3.0 40.0 + - - +
225B ILE* 3.0 14.3 + - - +
227B LYS* 6.3 0.2 - - - -
255B MET* 5.1 0.2 - - - +
260B LYS 5.7 0.8 + - - -
261B GLY* 4.9 2.3 - - - -
262B LEU 3.0 21.7 + - - +
403B FLC 5.7 0.2 - - - -
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Residues in contact with GLY 222 (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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196B ARG* 3.9 4.2 - - - +
198B GLY* 4.9 0.2 - - - -
199B ASP* 3.1 25.2 - - - +
220B GLY 3.1 0.6 + - - -
221B HIS* 1.3 72.9 - - - +
223B GLU* 1.3 57.6 + - - +
225B ILE* 3.1 1.7 + - - +
226B LEU* 2.8 40.0 + - - +
402B GLY 3.1 27.1 + - - -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO 3.7 18.4 - - - +
114A HIS* 2.9 26.7 + - - +
115A CYS* 3.5 27.3 + - + +
404A BME 5.4 1.1 - - + +
189B ILE* 3.9 1.9 - - - +
196B ARG* 2.8 39.6 + - - +
197B VAL 4.9 2.1 - - - +
198B GLY* 5.7 0.2 - - - -
221B HIS* 3.2 30.8 + - + -
222B GLY* 1.3 75.5 - - - +
224B SER* 1.3 62.2 + - - +
226B LEU* 3.4 2.1 + - - +
227B LYS* 3.0 42.3 + - - +
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Residues in contact with SER 224 (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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221B HIS* 3.0 28.5 + - - +
223B GLU* 1.3 77.9 - - - +
225B ILE* 1.3 58.0 + - - +
227B LYS* 3.2 6.3 + - - +
228B VAL* 3.0 34.7 + - - +
255B MET* 3.7 15.5 - - - -
259B VAL* 3.6 28.4 + - - +
260B LYS 4.8 0.2 + - - -
261B GLY* 3.3 17.3 - - - -
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Residues in contact with ILE 225 (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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199B ASP* 3.3 27.1 - - + +
205B ALA* 3.2 28.1 - - - +
218B THR* 3.8 5.6 - - - +
219B THR 3.5 28.5 - - - +
220B GLY* 3.6 15.9 - - - +
221B HIS 3.0 21.1 + - - +
222B GLY 3.1 5.8 + - - +
224B SER* 1.3 72.8 - - - +
226B LEU* 1.3 60.7 + - - +
228B VAL* 3.7 1.5 - - - -
229B ASN* 2.8 26.7 + - - -
230B LEU* 3.3 21.8 + - + -
255B MET* 3.6 22.9 - - + -
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Residues in contact with LEU 226 (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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115A CYS* 3.5 25.8 - - - -
116A PHE* 4.6 11.4 - - + -
202A CYS* 5.9 0.2 - - - -
203A LEU* 3.9 38.0 - - + +
208A TYR* 4.8 0.2 - - - -
197B VAL 4.4 7.2 - - - +
198B GLY* 3.9 18.2 - - - +
199B ASP* 3.8 6.7 - - - -
202B CYS* 3.8 34.8 - - + -
205B ALA* 3.8 11.9 - - + -
222B GLY 2.8 17.8 + - - +
223B GLU 3.6 4.0 - - - +
225B ILE* 1.3 77.8 - - - +
227B LYS* 1.3 62.8 + - - +
228B VAL 3.3 0.3 + - - -
229B ASN* 3.3 18.4 + - - +
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Residues in contact with LYS 227 (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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82A MET* 3.7 2.5 - - - +
86A ASP 4.7 2.0 + - - +
87A LEU* 3.2 44.8 - - + +
88A SER* 4.4 4.0 - - - +
89A ALA* 4.8 2.0 - - + +
115A CYS* 5.0 3.6 - - - -
203A LEU* 4.1 16.2 - - + -
208A TYR* 2.6 35.0 + - - -
404A BME 2.3 35.8 + - - +
223B GLU* 3.0 37.7 + - - +
224B SER* 3.2 7.4 + - - +
226B LEU* 1.3 74.5 - - - +
228B VAL* 1.3 52.8 - - - +
259B VAL* 4.3 21.0 + - + +
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Residues in contact with VAL 228 (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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87A LEU* 4.2 8.3 - - + -
208A TYR* 3.8 8.2 + - - -
232A ARG* 5.0 3.6 + - - -
224B SER 3.0 20.1 + - - +
225B ILE 3.7 4.9 - - - +
227B LYS* 1.3 79.6 - - - +
229B ASN* 1.3 69.4 + - - +
230B LEU* 3.8 19.5 - - + +
233B LEU* 3.9 15.2 - - + +
254B TYR* 3.8 35.2 - - + +
255B MET* 3.9 34.1 - - + -
259B VAL* 4.4 9.4 - - + -
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Residues in contact with ASN 229 (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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203A LEU 3.1 21.9 - - - +
204A GLY* 4.0 5.7 - - - -
208A TYR* 4.6 4.6 - - + -
229A ASN* 2.5 31.9 + - - -
232A ARG* 3.8 28.6 - - + +
236A PHE* 6.1 0.2 - - + -
203B LEU 5.5 0.7 - - - +
204B GLY 3.2 19.2 + - - +
205B ALA* 4.4 4.5 + - - +
225B ILE 2.8 15.5 + - - -
226B LEU* 3.3 13.4 + - - +
228B VAL* 1.3 75.7 - - - +
230B LEU* 1.3 58.1 + - - +
232B ARG* 3.2 6.4 + - + +
233B LEU* 2.8 25.6 + - + +
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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