Contacts of the strand formed by residues 417 - 422 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A LYS* 4.2 22.4 - - - +
341A GLU* 5.5 1.6 - - - +
343A LYS* 3.7 34.2 + - + +
344A ILE 3.2 8.3 - - - +
345A LEU* 3.8 21.8 - - + -
373A ARG* 3.5 4.0 - - - +
374A LYS* 2.7 52.4 + - + +
376A VAL* 4.2 21.7 + - - +
415A GLY 4.4 4.6 - - - +
416A ASP* 1.3 77.2 - - - +
418A LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LYS* 3.4 9.4 - - - +
344A ILE* 2.7 54.0 + - + +
346A VAL* 5.0 4.3 - - + -
354A ILE* 3.9 32.5 - - + -
371A ILE* 4.7 3.4 - - + -
372A GLN 3.3 13.0 - - - +
373A ARG* 4.4 1.8 - - - -
374A LYS* 6.0 0.2 - - - -
388A LEU* 3.8 25.1 - - + -
412A LEU* 4.0 28.5 - - + -
416A ASP* 6.4 0.2 - - + -
417A GLU* 1.3 78.1 - - - +
419A GLN* 1.3 60.2 + - - +
438A PHE* 3.8 15.9 - - + -
440A ALA* 4.4 7.0 - - + -
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PHE* 4.0 28.1 - - + -
342A ASN 5.6 1.3 - - - +
343A LYS* 4.0 25.7 - - + +
370A LEU 3.4 2.1 - - - +
371A ILE* 3.6 2.8 - - - -
372A GLN* 2.7 66.1 + - + +
374A LYS* 3.9 22.7 + - + +
385A LEU* 3.4 23.9 - - + +
418A LEU* 1.3 75.2 - - - +
420A LEU* 1.3 60.9 + - - +
438A PHE* 3.9 8.9 - - - -
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PHE* 3.3 23.6 - - - +
325A VAL* 4.2 14.2 + - + -
327A TRP* 3.8 31.5 + - + +
356A GLY* 4.0 20.2 - - - -
358A VAL* 3.7 26.2 - - + -
369A HIS* 3.6 42.2 - - + +
370A LEU 3.4 4.5 - - - +
371A ILE* 4.5 3.8 - - + +
419A GLN* 1.3 71.8 - - - +
421A ALA* 1.3 57.4 + - - +
422A ILE* 4.1 10.1 - - + -
437A PHE 4.5 0.7 - - - +
438A PHE* 3.8 18.0 - - + -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A TYR* 3.6 23.6 - - + -
324A PHE* 3.6 18.8 - - + -
369A HIS* 3.3 2.8 - - - -
370A LEU* 2.8 37.6 + - + +
372A GLN* 3.3 28.5 - - - +
419A GLN 3.9 0.4 - - - -
420A LEU* 1.3 72.4 - - - +
422A ILE* 1.3 62.9 + - - +
423A PRO* 3.5 4.3 - - - +
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Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A TYR* 3.3 4.8 - - - -
323A THR* 2.9 43.5 + - + +
325A VAL* 3.9 28.5 - - + -
358A VAL* 4.4 2.2 - - + -
360A TYR* 3.7 31.4 - - + +
367A MET* 4.3 1.6 - - + -
368A GLY 3.4 13.2 - - - +
369A HIS* 3.8 6.7 - - + -
420A LEU* 4.1 5.8 - - + -
421A ALA* 1.3 75.5 - - - +
423A PRO* 1.3 53.9 - - - +
424A ARG* 2.7 25.0 + - + -
427A ALA* 3.7 23.6 - - + -
429A ILE* 4.0 17.7 - - + -
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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