Contacts of the strand formed by residues 215 - 223 (chain B) in PDB entry 4ZCH
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 ALA 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B THR* 2.9 11.1 + - - +
214B TYR* 1.3 101.5 - - + +
216B MET* 1.3 69.5 + - - +
241B ILE* 3.5 23.6 - - + +
242B GLN 3.1 7.2 - - - +
243B ASN* 3.9 10.5 - - - +
273B ARG* 5.9 0.5 - - - +
401B ASN* 4.3 7.9 - - + -
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Residues in contact with MET 216 (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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209B TYR* 3.5 42.0 - - + -
211B ASP* 3.6 39.9 - - + +
213B THR* 3.8 17.7 - - - +
215B ALA* 1.3 75.8 - - - +
217B GLY* 1.3 57.8 + - - +
241B ILE* 4.1 3.1 - - - -
242B GLN* 2.7 42.6 + - - +
244B MET* 3.6 27.2 - - + +
271B ILE* 4.7 2.2 - - + -
273B ARG* 3.9 18.2 - - + -
276B ALA* 3.8 22.4 - - + -
277B GLN 4.3 1.3 - - - +
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Residues in contact with GLY 217 (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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209B TYR* 2.8 17.1 + - - -
216B MET* 1.3 78.0 - - - +
218B HIS* 1.3 59.9 + - - +
219B LEU* 5.8 0.4 - - - -
240B CYS 3.0 17.0 - - - -
241B ILE* 4.0 4.1 - - - +
271B ILE* 3.7 10.6 - - - +
272B PRO* 3.2 23.2 - - - +
273B ARG* 6.3 0.4 - - - +
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Residues in contact with HIS 218 (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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205B GLY* 3.5 20.5 + - - -
207B VAL* 3.5 19.4 - - + +
209B TYR* 2.8 23.2 + - - +
217B GLY* 1.3 72.3 - - - +
219B LEU* 1.3 68.3 + - - +
220B ILE* 4.6 8.9 - - + +
239B ARG* 3.4 5.3 - - - +
240B CYS* 2.9 50.2 + - + +
253B CYS* 3.0 28.6 + - - +
255B SER* 4.6 3.0 + - - -
269B LEU* 3.7 28.9 - - + -
270B ALA 3.4 11.9 - - - +
271B ILE* 3.9 5.6 - - + -
272B PRO* 4.4 0.4 - - - -
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Residues in contact with LEU 219 (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 TYR* 3.9 24.9 - - + +
217B GLY 5.8 0.2 - - - -
218B HIS* 1.3 77.4 - - - +
220B ILE* 1.3 62.6 + - - +
221B GLN* 3.5 35.4 - - + +
236B THR* 3.9 13.7 - - + +
238B PHE 3.7 3.8 - - - -
239B ARG* 3.7 32.5 - - + -
240B CYS 5.7 0.2 - - - +
268B GLN 3.7 0.3 - - - +
269B LEU* 3.2 8.5 - - - +
270B ALA* 2.8 35.0 + - + +
272B PRO* 4.1 18.2 - - + -
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Residues in contact with ILE 220 (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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203B ILE* 3.7 22.4 - - + -
204B TYR* 3.7 11.7 - - - +
205B GLY* 3.6 28.9 - - - +
218B HIS* 4.6 12.8 - - + +
219B LEU* 1.3 72.7 - - - +
221B GLN* 1.3 64.2 + - - +
236B THR* 3.7 2.4 - - - -
237B LEU* 2.8 36.2 + - + +
238B PHE* 2.9 40.7 + - + +
255B SER* 3.8 13.9 - - - +
267B LEU* 4.8 2.0 - - + -
268B GLN 3.7 2.7 - - - +
269B LEU* 4.8 2.7 - - + -
287B PHE* 4.3 18.4 - - + -
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Residues in contact with GLN 221 (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 TYR* 4.8 8.5 + - - -
219B LEU* 3.5 31.2 - - + +
220B ILE* 1.3 78.1 - - - +
222B ARG* 1.3 59.1 - - - +
234B LEU* 3.4 31.9 - - + +
235B VAL 3.3 6.5 - - - +
236B THR* 3.4 22.8 + - - +
237B LEU* 4.5 1.1 - - - -
267B LEU* 3.3 11.5 - - - +
268B GLN* 2.8 68.8 + - + +
270B ALA* 3.5 11.1 - - - +
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Residues in contact with ARG 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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221B GLN* 1.3 72.3 - - - +
223B LYS* 1.3 63.7 + - - +
224B LYS* 3.5 31.2 - - - +
233B SER 3.7 1.6 - - - +
234B LEU* 3.3 6.2 - - - +
235B VAL* 2.8 52.0 + - + +
237B LEU* 3.8 24.3 - - + +
260B LYS 3.5 21.2 + - - -
261B LEU* 3.7 22.4 - - + +
262B GLU* 3.6 18.8 + - - +
265B ASP* 2.8 33.3 + - + +
266B GLU 3.5 6.5 - - - +
267B LEU* 4.4 1.6 - - + -
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Residues in contact with LYS 223 (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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192B LYS* 4.2 21.6 - - - +
221B GLN 4.2 0.2 - - - -
222B ARG* 1.3 71.4 - - - +
224B LYS* 1.3 68.3 - - - +
225B VAL* 3.6 1.7 + - - -
233B SER* 3.7 11.9 - - - +
234B LEU* 4.0 17.5 - - + +
264B GLY 4.8 0.3 - - - +
265B ASP* 3.6 2.7 - - - -
266B GLU* 2.8 58.8 + - + +
268B GLN* 5.4 5.4 - - + +
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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