Contacts of the strand formed by residues 336 - 343 (chain B) in PDB entry 4ZPK
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 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ARG* 4.6 10.5 - - - -
248B HIS 3.7 8.5 - - - -
249B SER* 5.5 0.7 - - - +
250B MET* 3.6 3.9 - - - +
255B THR* 5.7 4.7 - - - -
325B VAL* 3.3 5.5 - - - +
326B ILE* 2.9 40.9 + - + -
335B GLN* 1.3 78.3 - - + +
337B ILE* 1.3 102.1 + - - +
338B MET* 3.6 18.4 - - - -
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 3.5 0.3 - - - -
248B HIS* 2.8 41.6 + - + +
249B SER 3.8 14.6 - - - +
250B MET* 3.6 34.5 - - + +
252B MET* 4.5 8.7 - - - -
293B HIS* 4.5 8.5 - - - +
296B LEU* 3.8 36.6 - - + -
297B CYS* 5.6 0.9 - - - -
324B THR 3.5 7.9 - - - +
325B VAL* 4.0 10.1 - - + -
336B CYS* 1.3 89.6 - - - +
338B MET* 1.3 64.1 + - - +
339B CYS* 4.1 18.4 - - - -
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Residues in contact with MET 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B HIS* 5.0 2.5 - - + -
232B PRO* 3.9 32.5 - - + +
233B SER* 5.2 7.0 - - - +
245B LEU* 5.5 4.7 - - + -
246B SER 3.8 3.4 - - - +
247B ARG* 2.9 53.8 - - + +
322B GLN 3.8 1.2 - - - +
323B GLY* 3.5 2.1 - - - -
324B THR* 2.9 36.8 + - - +
326B ILE* 3.7 29.4 - - + +
336B CYS* 3.6 12.3 - - - -
337B ILE* 1.3 78.1 - - - +
339B CYS* 1.3 62.1 + - - +
340B VAL* 5.6 0.6 - - - +
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Residues in contact with CYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.4 8.5 - - - +
246B SER* 2.8 49.6 + - - +
248B HIS* 3.5 25.6 - - - -
252B MET* 4.5 9.9 - - - -
296B LEU* 5.6 1.1 - - - -
321B THR* 3.7 26.5 - - + -
322B GLN 3.4 2.9 - - - -
323B GLY* 4.3 5.4 - - - -
337B ILE* 4.1 11.9 - - - -
338B MET* 1.3 80.0 - - - +
340B VAL* 1.3 62.5 + - - +
341B ASN* 3.4 6.3 - - - +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN* 5.4 12.3 - - - +
232B PRO* 4.5 28.5 - - + -
239B LEU* 4.0 28.0 - - + -
243B THR* 4.3 4.7 - - + -
244B PHE 4.1 2.9 - - - +
245B LEU* 4.8 9.2 - - + -
322B GLN* 2.9 47.9 + - + +
338B MET 5.6 0.4 - - - +
339B CYS* 1.3 71.8 - - - +
341B ASN* 1.3 59.9 + - - +
342B TYR* 3.4 32.4 + - + +
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Residues in contact with ASN 341 (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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243B THR* 3.2 3.6 - - - +
244B PHE* 2.9 87.6 + - + +
246B SER* 3.3 22.5 + - - -
248B HIS* 5.1 1.4 + - - -
307B TYR* 4.5 1.6 + - - -
309B MET* 6.1 1.2 - - - +
319B LEU* 4.8 7.2 - - + +
320B GLU 3.9 4.3 - - - -
321B THR* 2.7 25.9 + - - +
339B CYS* 3.4 17.2 - - - +
340B VAL* 1.3 70.7 - - - +
342B TYR* 1.3 61.5 + - - +
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Residues in contact with TYR 342 (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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220A LYS* 5.2 3.4 - - - +
224A GLN* 6.3 0.4 - - - -
262A SER 4.7 12.4 + - - -
263A PHE* 4.8 8.5 - - + -
264A ILE* 4.1 28.0 - - + -
230B GLN* 5.1 2.4 + - - +
237B ILE* 3.9 23.0 - - + +
239B LEU* 4.7 4.1 - - + +
243B THR* 3.9 22.7 - - + +
319B LEU* 3.3 6.8 - - - +
320B GLU* 2.8 49.0 + - + +
322B GLN* 3.9 29.4 + - + -
340B VAL* 3.4 36.3 - - + +
341B ASN* 1.3 74.5 - - - +
343B VAL* 1.3 61.7 + - - +
344B LEU* 3.8 3.8 - - + +
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Residues in contact with VAL 343 (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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220A LYS* 3.8 12.8 - - - -
264A ILE* 4.8 0.5 - - - +
242B LYS* 2.8 46.7 + - + +
243B THR* 4.5 0.6 + - - -
244B PHE* 4.0 22.9 - - + -
264B LEU* 4.4 15.7 - - + -
265B ILE* 5.3 7.4 - - + -
317B VAL* 4.8 8.7 - - + -
318B TRP 3.9 9.2 - - - +
319B LEU* 3.6 19.7 - - + -
341B ASN 4.6 0.4 - - - +
342B TYR* 1.3 76.0 - - - +
344B LEU* 1.3 67.4 + - - +
345B SER 3.9 18.4 - - - +
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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