Contacts of the strand formed by residues 250 - 257 (chain B) in PDB entry 3ZZY
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 CYS 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ASN* 3.4 14.8 - - - +
192B PHE* 3.7 17.5 - - + -
193B TYR* 4.4 9.9 - - - -
245B ASN* 3.2 14.7 - - - +
246B ILE 3.7 0.2 + - - -
247B TYR* 3.2 34.3 + - - +
248B ASN 3.2 5.8 + - - +
249B ALA* 1.3 80.7 - - - +
251B CYS* 1.3 112.1 + - - +
252B THR* 3.5 2.7 - - - -
504D PRO* 5.8 0.9 - - - -
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Residues in contact with CYS 251 (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 VAL* 3.6 16.4 - - + -
189B GLU 3.2 9.2 + - - -
190B ASN* 2.8 12.4 + - - +
191B LEU* 4.3 2.0 - - - -
192B PHE 3.9 4.3 - - - -
193B TYR 3.7 23.8 - - - -
195B VAL* 4.1 6.3 - - + -
246B ILE* 3.0 43.1 + - + +
247B TYR* 4.2 6.7 - - - +
250B CYS* 1.3 112.6 - - - +
252B THR* 1.3 62.5 + - - +
253B LEU 3.7 0.2 + - - -
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Residues in contact with THR 252 (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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187B ILE 3.5 0.5 - - - +
188B VAL* 3.4 3.3 - - - -
189B GLU* 2.8 39.5 + - - +
190B ASN* 3.0 27.7 + - - +
243B GLY* 3.6 28.3 - - - +
244B GLN 3.6 1.3 - - - -
245B ASN* 2.7 22.1 + - - +
250B CYS* 4.4 1.2 - - - -
251B CYS* 1.3 70.7 - - - +
253B LEU* 1.3 64.8 + - - +
254B ARG* 3.7 26.3 + - - +
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Residues in contact with LEU 253 (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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186B ILE* 3.7 25.1 - - + -
187B ILE 3.7 1.6 - - - -
188B VAL* 4.1 8.5 - - + -
200B LEU* 4.6 2.0 - - + -
203B ILE* 5.0 1.1 - - + -
204B PHE* 4.2 22.7 - - + -
241B LEU* 3.7 31.2 - - + +
242B ASP* 3.6 0.2 - - - +
243B GLY* 2.7 32.6 + - - -
244B GLN 3.0 18.7 + - - +
246B ILE* 4.0 26.0 - - + -
252B THR* 1.3 70.9 - - - +
254B ARG* 1.3 63.1 + - - +
255B ILE* 4.0 7.4 - - + -
500D LEU* 4.0 23.8 - - + -
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Residues in contact with ARG 254 (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 ARG 3.7 1.2 - - - +
186B ILE* 3.5 5.2 - - - -
187B ILE* 2.8 48.7 + - + +
189B GLU* 2.8 46.0 + - + +
190B ASN* 5.2 4.6 - - - +
242B ASP* 3.5 7.1 + - - -
243B GLY* 4.0 18.6 - - - +
252B THR* 3.9 23.3 - - - +
253B LEU* 1.3 75.9 - - - +
255B ILE* 1.3 61.5 + - - +
256B ASP* 4.3 5.8 - - - +
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Residues in contact with ILE 255 (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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184B LEU* 3.9 34.1 - - + -
185B ARG 3.6 5.4 - - - +
186B ILE* 4.4 11.7 - - + -
204B PHE* 3.9 19.7 - - + -
237B ALA 4.0 6.3 - - - +
238B LYS* 3.5 29.2 - - + +
241B LEU* 3.6 32.3 - - + +
242B ASP* 2.9 32.0 + - + +
253B LEU* 4.3 6.7 - - + -
254B ARG* 1.3 81.3 - - - +
256B ASP* 1.3 75.6 + - - +
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Residues in contact with ASP 256 (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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184B LEU* 3.5 9.7 - - - +
185B ARG* 2.8 38.4 + - + +
238B LYS* 4.0 10.8 - - - +
254B ARG* 4.3 5.4 - - - +
255B ILE* 1.3 95.1 + - - +
257B PHE* 1.3 67.9 + - - +
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Residues in contact with PHE 257 (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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180B GLN* 4.5 22.0 - - - +
181B SER* 4.1 22.7 - - - -
183B VAL 3.9 2.9 - - - +
184B LEU* 3.8 21.8 - - + -
185B ARG* 4.3 4.0 - - - +
234B ALA 4.1 0.9 - - - -
235B GLN* 3.8 44.6 - - + -
238B LYS* 3.4 30.0 - - + +
256B ASP* 1.3 80.5 - - - +
258B SER* 1.3 65.7 + - - +
259B LYS* 4.2 1.7 + - - +
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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