Contacts of the strand formed by residues 415 - 422 (chain A) in PDB entry 1ZMC
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 VAL 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ILE* 4.5 7.2 - - + -
407A LEU 3.7 5.2 - - - +
408A GLY* 4.4 1.6 - - - -
414A ARG* 1.3 73.4 - - - +
416A LEU* 1.3 66.1 + - - +
417A GLY 3.9 22.2 - - - +
418A ALA* 5.2 6.1 - - + -
432A ALA* 6.0 0.7 - - + +
435A ALA* 5.5 3.4 - - + -
436A LEU* 3.1 29.9 - - + +
439A GLY* 6.0 0.7 - - - -
440A ALA* 3.0 18.3 + - + +
441A SER 3.9 9.6 - - - -
442A CYS* 3.9 5.6 - - - +
445A ILE* 3.7 21.1 - - + -
459A PHE* 6.1 1.6 - - + -
463A ASN* 3.5 22.9 - - - +
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Residues in contact with LEU 416 (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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352A ASN* 4.8 2.4 + - - +
368A GLY* 3.3 6.9 - - - -
369A LYS* 2.8 27.8 + - + +
374A LEU* 3.7 31.2 - - + -
379A ILE* 3.6 30.3 - - + -
381A TYR* 4.3 0.9 - - + -
407A LEU* 2.7 10.7 + - - +
408A GLY 4.1 4.0 - - - +
409A GLN* 3.8 27.1 - - + +
414A ARG* 3.7 16.8 - - + +
415A VAL* 1.3 78.6 - - - +
417A GLY* 1.3 59.2 + - - +
436A LEU* 4.1 8.1 - - - +
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Residues in contact with GLY 417 (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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367A VAL 3.5 11.7 - - - -
368A GLY* 4.1 0.2 - - - -
369A LYS 3.6 15.3 - - - -
406A ILE* 3.7 2.9 - - - -
407A LEU* 3.0 30.0 + - - +
415A VAL* 3.7 10.5 - - - +
416A LEU* 1.3 82.0 - - - +
418A ALA* 1.3 60.3 + - - +
419A HIS* 4.1 5.6 - - - -
436A LEU* 5.1 1.3 - - - -
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Residues in contact with ALA 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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366A TRP* 3.2 26.3 - - - +
367A VAL* 3.1 13.1 + - + +
405A LYS 3.6 5.8 - - - -
406A ILE* 3.8 17.9 - - + -
415A VAL* 5.2 4.7 - - + -
417A GLY* 1.3 73.9 - - - +
419A HIS* 1.3 63.2 + - - +
420A ILE* 4.2 7.6 - - + +
432A ALA* 3.8 28.7 - - + -
436A LEU* 5.6 0.9 - - + +
459A PHE* 4.1 4.3 - - + -
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Residues in contact with HIS 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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219A ASP* 3.7 21.9 + - + +
222A ILE* 3.6 25.0 - - + +
365A ALA 3.6 3.8 - - - -
366A TRP* 3.3 33.8 - + + +
367A VAL 4.8 2.0 - - - -
368A GLY 5.0 0.2 - - - -
369A LYS 2.5 32.4 + - - -
370A SER* 3.6 15.4 - - - -
403A MET 3.8 1.6 - - - +
404A VAL* 3.6 2.1 - - - +
405A LYS* 2.9 47.7 + - + +
406A ILE* 5.1 0.4 - - - +
407A LEU* 3.6 17.6 - - + +
418A ALA* 1.3 84.1 + - - +
420A ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 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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222A ILE* 4.9 2.1 - - - +
364A VAL* 3.2 8.9 - - - +
365A ALA 2.8 45.2 + - - +
388A PHE* 4.0 26.0 - - + -
403A MET 3.6 1.6 - - - -
404A VAL* 4.0 18.2 - - + -
418A ALA* 5.0 8.7 - - + -
419A HIS* 1.3 81.1 - - - +
421A LEU* 1.3 63.8 + - - +
422A GLY 4.0 0.2 - - - -
425A ALA* 3.6 25.8 - - + +
428A MET* 4.1 21.5 - - + -
429A VAL* 4.0 34.3 - - + +
432A ALA* 5.2 0.7 - - + -
459A PHE* 5.1 4.0 - - + -
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Residues in contact with LEU 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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222A ILE* 3.8 25.4 - - + +
225A ASN* 3.6 35.4 - - + +
226A PHE* 3.7 43.1 - - + +
229A ILE* 4.1 9.0 - - + -
362A PRO* 4.1 9.0 - - + -
363A GLU 3.6 10.8 - - - +
364A VAL* 3.9 5.4 - - + -
388A PHE* 3.4 3.6 - - - -
402A GLY* 2.9 11.2 - - - -
403A MET* 2.6 45.6 + - + +
419A HIS 4.2 0.4 - - - -
420A ILE* 1.3 75.0 - - - +
422A GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 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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362A PRO* 3.5 13.0 - - - +
363A GLU* 2.9 36.3 + - - +
388A PHE* 3.7 3.4 - - - -
401A ASP 3.1 9.2 - - - -
420A ILE 4.0 1.2 - - - -
421A LEU* 1.3 76.6 - - - +
423A PRO* 1.3 76.3 - - - +
425A ALA* 3.7 3.8 - - - +
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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