Contacts of the strand formed by residues 417 - 422 (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 GLU 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LYS* 4.3 22.0 + - - +
341B GLU* 6.1 0.5 - - - +
343B LYS* 3.5 46.1 + - + +
344B ILE 3.4 4.7 - - - +
345B LEU* 4.2 13.7 - - + -
372B GLN 3.7 0.5 - - - +
373B ARG* 3.5 5.2 - - - +
374B LYS* 3.0 47.2 + - + +
376B VAL* 5.4 8.1 + - - +
415B GLY 4.1 7.5 - - - +
416B ASP* 1.3 79.0 - - - +
418B LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 418 (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 LEU* 5.5 0.2 - - + -
343B LYS* 3.5 9.8 - - - +
344B ILE* 2.8 53.1 + - + +
346B VAL* 4.8 3.6 - - + -
354B ILE* 3.7 33.2 - - + -
371B ILE* 4.8 3.4 - - + -
372B GLN 3.3 13.5 - - - +
373B ARG* 4.2 3.8 - - + -
388B LEU* 3.6 26.5 - - + -
412B LEU* 3.7 28.5 - - + -
417B GLU* 1.3 74.6 - - - +
419B GLN* 1.3 60.3 + - - +
438B PHE* 3.8 16.3 - - + -
440B ALA* 4.5 7.0 - - + -
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Residues in contact with GLN 419 (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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319B LYS* 5.1 2.8 + - - -
322B TYR* 5.9 0.4 - - - -
324B PHE* 3.9 32.7 - - + -
342B ASN 5.7 1.8 - - - +
343B LYS* 3.6 31.5 - - + +
370B LEU 3.3 2.9 - - - +
371B ILE* 3.5 1.7 - - - -
372B GLN* 2.8 71.5 + - + +
374B LYS* 4.1 19.8 + - + +
385B LEU* 3.7 18.6 - - + +
417B GLU 5.8 0.2 - - - -
418B LEU* 1.3 76.0 - - - +
420B LEU* 1.3 58.5 + - - +
438B PHE* 3.8 9.6 - - - -
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Residues in contact with LEU 420 (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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323B THR 4.4 2.3 - - - +
324B PHE* 3.4 20.2 - - - -
325B VAL* 4.1 10.6 + - + +
327B TRP* 4.2 21.7 + - + +
356B GLY* 4.1 20.2 - - - -
358B VAL* 3.4 31.0 - - + -
369B HIS* 3.7 39.7 - - + +
370B LEU 3.4 3.8 - - - +
371B ILE* 4.4 4.3 - - + +
419B GLN* 1.3 72.2 - - - +
421B ALA* 1.3 57.4 + - - +
422B ILE* 3.8 11.0 + - + +
437B PHE 4.5 1.6 - - - +
438B PHE* 3.9 24.3 - - + -
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Residues in contact with ALA 421 (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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322B TYR* 3.4 28.5 - - + -
324B PHE* 3.7 16.4 - - + -
369B HIS* 3.2 4.6 - - - -
370B LEU* 2.8 40.4 + - + +
372B GLN* 3.6 24.5 - - - +
419B GLN* 3.9 0.6 + - - +
420B LEU* 1.3 72.4 - - - +
422B ILE* 1.3 61.1 + - - +
423B PRO* 3.5 3.0 - - - +
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Residues in contact with ILE 422 (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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322B TYR* 3.3 5.8 - - - -
323B THR* 2.8 62.2 + - + +
325B VAL* 3.7 28.7 - - + -
358B VAL* 4.5 7.2 - - + -
360B TYR* 3.6 28.7 - - + +
367B MET* 4.3 6.7 - - + -
368B GLY 3.5 12.8 - - - +
369B HIS* 3.9 3.1 - - + -
420B LEU* 3.8 13.7 - - + +
421B ALA* 1.3 74.3 - - - +
423B PRO* 1.4 58.8 - - + +
424B ARG* 2.9 12.2 + - + +
427B ALA* 3.7 25.1 - - + -
429B ILE* 4.8 6.3 - - + -
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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