Contacts of the strand formed by residues 235 - 243 (chain C) in PDB entry 1ZVM
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 VAL 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C ALA 3.4 22.7 - - - +
202C ASP 3.4 6.5 - - - +
204C VAL* 3.7 20.2 - - + -
230C LEU* 4.3 12.8 - - + -
231C GLN 2.7 26.9 + - - +
232C PRO 3.2 18.0 - - - +
234C LYS* 1.3 77.6 - - - +
236C GLN* 1.3 65.1 + - - +
237C THR 3.4 25.8 - - - +
238C LEU* 5.2 1.6 - - + -
270C ASN 5.0 0.7 - - - +
271C ILE* 3.9 28.7 - - + +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASP* 2.5 61.1 + - - +
203C VAL* 3.8 8.3 - - - +
234C LYS 4.0 3.3 - - - +
235C VAL* 1.3 75.9 - - - +
237C THR* 1.3 72.8 + - + +
271C ILE* 3.6 3.2 - - - +
272C GLN* 2.9 26.2 + - - +
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Residues in contact with THR 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASP 3.0 6.2 + - - +
203C VAL* 4.1 23.3 - - + +
204C VAL 3.0 24.9 + - - -
235C VAL* 3.4 10.0 - - - +
236C GLN* 1.3 94.2 - - + +
238C LEU* 1.3 65.1 + - - +
239C GLU* 4.2 1.0 + - - +
271C ILE* 3.7 2.2 - - - -
272C GLN* 3.0 31.0 - - + -
273C PHE* 5.1 0.7 - - - -
274C SER* 4.8 8.7 - - - -
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 5.0 0.9 - - + -
204C VAL* 3.3 24.5 - - + +
206C VAL* 4.1 24.9 - - + -
222C PHE* 4.3 13.0 - - + -
230C LEU* 4.0 19.5 - - + -
235C VAL* 5.4 0.4 - - + -
237C THR* 1.3 74.1 + - - +
239C GLU* 1.3 59.9 + - - +
262C LEU* 4.2 10.3 - - + -
266C ILE* 3.3 44.9 - - + -
271C ILE* 4.0 3.5 - - + +
272C GLN 2.7 11.2 + - - +
273C PHE* 3.3 20.2 - - + -
274C SER 2.9 22.5 + - - -
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 4.8 4.0 - - + -
204C VAL 2.9 8.4 + - - +
205C HIS* 3.0 31.5 + - + +
206C VAL* 3.0 25.2 + - - +
237C THR* 4.1 4.2 - - - +
238C LEU* 1.3 73.9 - - - +
240C ALA* 1.3 64.7 + - - +
241C TRP* 2.8 32.2 + - + +
274C SER* 3.2 31.8 + - - +
276C LYS* 3.3 24.7 - - + +
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C VAL* 3.3 22.4 - - + +
208C LEU* 4.1 17.5 - - + -
238C LEU 4.0 1.0 + - - -
239C GLU* 1.3 73.5 - - - +
241C TRP* 1.3 64.2 + - - +
242C VAL* 3.8 2.2 - - + -
259C ILE* 5.3 0.4 - - + -
262C LEU* 4.5 1.1 - - + -
273C PHE* 4.1 23.1 - - + -
274C SER 2.9 7.6 + - - +
275C CYS* 3.4 9.3 - - - -
276C LYS 2.9 26.5 + - - +
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Residues in contact with TRP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C LEU* 4.6 13.0 - - + -
135C PHE* 3.6 43.3 - + - -
142C MET* 4.9 5.4 - - + -
205C HIS* 3.4 33.5 - + + -
206C VAL 2.8 11.9 + - - +
207C MET* 3.5 25.0 - - + -
208C LEU 2.9 23.7 + - - -
239C GLU* 2.8 29.9 + - + -
240C ALA* 1.3 79.5 - - - +
242C VAL* 1.3 63.2 + - - +
243C ILE* 3.4 5.9 + - + +
276C LYS* 3.5 16.0 - - + +
278C ILE* 3.5 21.1 - - + -
284C PHE* 4.0 15.5 - + - -
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.8 5.6 - - + -
210C GLY* 3.6 26.0 - - - +
215C ILE* 4.1 10.3 - - + -
240C ALA* 4.7 4.5 - - + -
241C TRP* 1.3 71.2 - - - +
243C ILE* 1.3 63.7 + - - +
244C HIS* 3.5 4.3 - - - -
253C LEU* 3.7 27.6 - - + +
254C CYS* 4.2 1.6 - - - -
259C ILE* 3.8 21.1 - - + -
275C CYS* 3.7 28.3 - - - -
276C LYS 2.9 11.3 + - - +
277C ASN* 4.7 4.3 - - - +
278C ILE 2.9 24.6 + - - -
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Residues in contact with ILE 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 3.7 14.4 - - + -
131C LEU* 3.5 31.6 - - + -
207C MET* 3.6 24.2 - - + -
208C LEU 2.8 19.4 + - - +
209C ASP* 3.9 2.1 - - - +
210C GLY* 2.8 29.5 + - - -
211C SER 4.1 0.5 + - - -
241C TRP 3.8 7.0 - - - +
242C VAL* 1.3 72.3 - - - +
244C HIS* 1.3 70.0 + - - +
245C GLY 4.0 0.2 + - - -
278C ILE* 3.5 38.6 - - + +
281C PRO* 3.7 20.2 - - + -
284C PHE* 5.6 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