Contacts of the strand formed by residues 254 - 260 (chain F) in PDB entry 1ZMC
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 ILE 254 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164F THR* 3.4 41.5 - - - +
165F ILE* 3.5 20.6 - - + -
246F ALA* 4.0 25.1 - - + -
247F THR 3.6 10.3 - - - +
248F LYS* 4.7 9.9 - - + -
252F GLY 4.5 3.6 - - - +
253F LYS* 1.3 81.6 - - - +
255F ASP* 1.3 66.7 + - - +
256F VAL* 3.9 8.2 + - + -
269F ILE 3.6 1.7 - - - +
270F THR* 3.3 6.3 - - - -
271F CYS* 2.9 40.2 + - - +
272F ASP 4.1 7.2 - - - +
273F VAL* 4.4 0.2 - - - -
274F LEU* 4.1 11.9 - - + +
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Residues in contact with ASP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F ALA* 3.0 5.9 - - - -
247F THR* 3.0 42.0 + - - +
249F LYS* 2.9 36.2 + - + +
254F ILE* 1.3 70.9 - - - +
256F VAL* 1.3 62.7 + - - +
257F SER* 3.9 1.8 + - - -
268F VAL* 3.7 21.6 - - + +
269F ILE 3.5 3.4 - - - -
270F THR* 2.8 25.3 + - - -
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F VAL* 4.6 5.6 - - + -
243F VAL* 3.5 41.3 - - + -
245F GLY 3.4 5.4 - - - +
246F ALA* 4.7 1.1 - - + -
254F ILE* 4.3 6.3 - - + +
255F ASP* 1.3 76.1 - - - +
257F SER* 1.3 60.7 + - - +
258F ILE* 3.5 7.2 + - + -
268F VAL* 3.5 6.7 - - - -
269F ILE* 2.8 50.7 + - + +
271F CYS* 4.3 17.3 - - - -
274F LEU* 4.0 28.5 - - + -
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Residues in contact with SER 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F VAL* 3.4 1.9 - - - +
244F THR* 2.6 43.1 + - - -
245F GLY* 2.8 30.2 + - - -
247F THR* 5.5 1.9 + - - -
255F ASP 3.9 2.3 + - - -
256F VAL* 1.3 70.1 - - - +
258F ILE* 1.3 58.5 + - - +
267F GLU 3.9 6.3 - - - -
268F VAL* 4.9 7.0 - - - +
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Residues in contact with ILE 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F VAL* 4.4 5.6 - - + -
238F LYS* 4.3 13.2 - - + -
241F THR* 3.8 17.0 - - + -
242F LYS 3.3 12.6 - - - +
243F VAL* 4.0 19.1 - - + -
244F THR 4.4 0.4 - - - +
256F VAL* 4.0 13.2 - - + +
257F SER* 1.3 81.7 - - - +
259F GLU* 1.3 69.7 + - - +
266F ALA* 3.2 5.0 - - - +
267F GLU* 2.8 63.8 + - + +
268F VAL* 4.4 0.9 - - - +
269F ILE* 4.1 29.4 - - + -
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Residues in contact with GLU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F THR* 3.5 6.8 - - - -
242F LYS* 2.8 57.5 + - + +
244F THR* 3.3 27.0 + - - +
258F ILE* 1.3 82.7 - - - +
260F ALA* 1.3 61.1 + - - +
263F GLY* 4.0 0.7 - - - -
264F GLY* 3.1 34.5 + - - +
265F LYS 3.5 10.1 - - - -
266F ALA* 3.8 13.9 - - - +
267F GLU* 5.9 0.2 - - - -
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Residues in contact with ALA 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ASN 3.5 10.8 - - - +
241F THR* 4.3 2.0 - - - +
242F LYS* 3.6 7.6 + - - -
259F GLU* 1.3 74.4 - - - +
261F ALA* 1.3 66.9 + - - +
262F SER* 4.2 5.4 - - - +
263F GLY* 3.0 18.8 + - - +
264F GLY 2.8 15.9 + - - +
265F LYS* 4.1 14.0 + - + +
299G ARG* 3.3 29.4 - - - +
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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