Contacts of the strand formed by residues 344 - 349 (chain B) in PDB entry 5ZOJ
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 GLU 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B TYR* 3.4 3.0 - - - -
341B ILE* 2.8 35.4 + - - +
342B GLY 3.6 9.0 - - - +
343B GLY* 1.3 78.5 - - - +
345B VAL* 1.3 64.2 + - - +
346B PHE* 3.2 23.1 - - + -
383B LYS* 3.2 35.4 + - + -
385B PHE 3.3 11.2 - - - +
386B ASN* 2.9 32.9 + - + +
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Residues in contact with VAL 345 (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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274B TRP* 3.7 30.1 - - + -
338B LEU* 5.3 1.3 - - + -
339B TYR 3.5 9.2 - - - +
340B TYR* 3.6 22.9 - - + -
344B GLU* 1.3 77.9 - - - +
346B PHE* 1.3 68.4 + - - +
383B LYS* 3.7 3.6 - - - +
384B ILE* 2.9 48.2 + - + -
385B PHE* 3.0 30.2 + - + +
440B LEU* 5.0 2.5 - - + -
442B LEU* 4.1 13.2 - - + -
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Residues in contact with PHE 346 (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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337B ARG 3.5 1.1 - - - +
338B LEU* 3.4 10.2 - - - +
339B TYR* 3.1 67.9 + + + +
341B ILE* 3.5 25.1 - - + -
344B GLU* 3.2 40.2 - - + -
345B VAL* 1.3 77.2 - - - +
347B ALA* 1.3 60.0 + - - +
381B ASN* 3.5 24.2 - - - +
382B LEU 3.3 5.2 - - - +
383B LYS* 3.8 32.3 - - + -
384B ILE* 4.1 3.8 - - - -
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Residues in contact with ALA 347 (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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336B VAL* 4.4 5.6 - - + -
337B ARG 3.5 4.0 - - - -
338B LEU* 4.0 15.7 - - + -
346B PHE* 1.3 74.6 - - - +
348B GLU* 1.3 61.0 + - - +
349B CYS 4.3 0.4 - - - -
357B VAL* 4.4 7.9 - - + -
376B ILE* 4.0 20.1 - - + +
380B CYS 4.0 0.2 - - - +
381B ASN* 3.4 4.1 - - - -
382B LEU* 2.9 33.3 + - - -
384B ILE* 3.7 24.4 - - + +
416B MET* 4.5 0.2 - - + -
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Residues in contact with GLU 348 (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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336B VAL* 3.3 7.2 - - - +
337B ARG* 2.8 61.3 + - + +
339B TYR* 4.4 10.2 - - + -
347B ALA* 1.3 74.5 - - - +
349B CYS* 1.3 62.1 + - - +
350B LEU* 3.3 28.4 + - + +
355B ILE* 4.4 0.2 - - - -
379B GLY* 5.0 8.4 - - - +
380B CYS 3.5 11.7 - - - +
381B ASN* 3.8 14.3 - - + +
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Residues in contact with CYS 349 (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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335B GLY 4.0 1.1 - - - -
347B ALA 4.3 0.2 - - - -
348B GLU* 1.3 69.0 - - - +
350B LEU* 1.3 63.0 + - - +
351B SER 3.9 7.2 - - - -
353B SER 3.2 26.9 - - - -
355B ILE* 3.6 32.6 - - + +
376B ILE* 3.7 19.0 - - + +
377B PRO 3.5 15.3 - - - +
378B PRO* 3.7 13.0 - - - +
379B GLY* 2.9 26.3 + - - -
380B CYS 3.3 7.7 + - - -
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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