Contacts of the strand formed by residues 327 - 333 (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 TRP 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LEU* 4.0 29.4 - - + -
309B ILE 3.5 24.0 - - - -
310B ALA* 3.5 15.9 - - - -
311B ASP* 4.4 2.5 - - - +
325B VAL* 3.5 48.6 + - + +
326B PRO* 1.3 73.6 - - - +
328B LEU* 1.3 66.6 + - - +
339B GLU* 5.7 0.9 - - - +
342B ASN* 2.8 46.7 + - - +
357B GLN 4.8 0.7 - - - -
420B LEU* 4.2 21.2 + - + +
436B THR* 3.8 11.0 - - + -
437B PHE* 3.7 25.6 - - - -
438B PHE* 3.7 34.0 - + + -
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Residues in contact with LEU 328 (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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308B LEU* 3.3 9.0 - - - +
309B ILE* 2.8 46.4 + - + +
310B ALA 4.0 5.6 - - - +
311B ASP* 3.5 48.9 - - + +
312B SER* 5.1 1.6 - - - +
327B TRP* 1.3 75.4 - - - +
329B LEU* 1.3 61.0 + - - +
339B GLU* 5.1 1.3 - - - -
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Residues in contact with LEU 329 (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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306B LEU* 4.3 11.2 - - + -
307B GLN 4.2 3.1 - - - +
308B LEU* 3.9 6.5 - - - +
309B ILE* 4.5 6.0 - - - +
328B LEU* 1.3 74.0 - - - +
330B SER* 1.3 63.8 + - - +
331B PHE* 3.6 34.3 - - - +
332B LYS* 4.0 16.6 - - + +
339B GLU* 3.6 38.9 + - + +
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Residues in contact with SER 330 (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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307B GLN* 2.8 48.7 + - - -
309B ILE* 3.9 30.0 - - - +
328B LEU 3.6 2.8 + - - -
329B LEU* 1.3 78.5 - - - +
331B PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 331 (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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200B TYR* 3.4 32.1 - + + +
258B ILE* 3.5 34.5 - - + -
259B ALA* 5.6 1.8 - - - -
260B LYS 6.0 0.7 - - - -
305B CYS* 3.4 40.4 - - + -
306B LEU* 3.3 2.8 - - - -
307B GLN* 2.9 71.7 + - + +
329B LEU* 3.6 11.6 - - - +
330B SER* 1.3 84.2 - - - +
332B LYS* 1.3 68.6 + - - +
333B ARG* 4.2 1.1 - - + -
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Residues in contact with LYS 332 (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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200B TYR* 4.7 5.5 + - - -
305B CYS 3.5 6.7 - - - +
306B LEU* 3.8 17.3 - - + +
329B LEU* 4.0 17.1 - - + +
331B PHE* 1.3 78.4 - - - +
333B ARG* 1.3 63.3 + - - +
334B GLY 3.5 22.5 + - - +
335B SER* 5.1 3.1 - - - +
337B LEU 3.7 19.1 - - - +
338B GLU* 4.5 13.2 - - + -
339B GLU* 5.5 2.9 - - + +
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Residues in contact with ARG 333 (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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200B TYR* 3.6 40.3 - - + +
292B LEU* 3.6 24.7 + - - +
293B LEU 2.8 29.3 + - - -
294B GLY* 2.9 28.5 + - - -
302B THR* 3.5 17.4 + - + +
303B GLN 2.8 34.0 + - - +
304B ASP* 3.3 4.4 - - - +
305B CYS* 2.8 45.2 + - - +
331B PHE* 4.2 7.9 - - + -
332B LYS* 1.3 74.5 - - - +
334B GLY* 1.3 65.6 + - - +
337B LEU* 5.5 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