Contacts of the strand formed by residues 415 - 422 (chain H) in PDB entry 1ZMD
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406H ILE* 4.5 8.3 - - + -
407H LEU 3.8 4.7 - - - +
414H ARG* 1.3 84.8 - - - +
416H LEU* 1.3 60.7 + - - +
417H GLY 3.9 18.6 - - - +
418H ALA* 4.9 5.8 - - + +
432H ALA* 6.3 0.2 - - + -
435H ALA* 5.1 1.6 - - + -
436H LEU* 3.7 36.1 - - + +
439H GLY* 5.9 0.2 - - - -
440H ALA 3.0 20.0 + - - +
441H SER 3.6 20.4 - - - +
442H CYS* 3.6 8.1 - - - +
445H ILE* 3.8 13.5 - - + -
459H PHE* 5.9 1.3 - - + -
463H ASN* 3.7 15.9 - - - +
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Residues in contact with LEU 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H ASN* 4.9 2.6 + - - -
368H GLY* 3.5 5.5 - - - -
369H LYS* 2.8 26.0 + - + +
374H LEU* 4.0 28.0 - - + -
379H ILE* 3.8 24.7 - - + -
381H TYR* 4.4 1.1 - - + -
407H LEU* 2.7 15.3 + - - +
408H GLY 4.0 4.0 - - - +
409H GLN* 3.6 45.8 - - + +
414H ARG* 3.6 23.1 - - - +
415H VAL* 1.3 77.3 - - - +
417H GLY* 1.3 55.6 + - - +
436H LEU* 4.5 4.8 - - - +
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Residues in contact with GLY 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367H VAL 3.4 10.8 - - - -
369H LYS 3.5 18.2 - - - -
406H ILE* 3.6 2.8 - - - -
407H LEU* 2.9 31.4 + - - +
415H VAL* 3.7 9.1 - - - +
416H LEU* 1.3 79.2 - - - +
418H ALA* 1.3 61.3 + - - +
419H HIS* 4.0 6.3 - - - -
436H LEU* 5.3 0.7 - - - -
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Residues in contact with ALA 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365H ALA 4.1 0.2 - - - +
366H TRP* 3.1 6.8 - - - +
367H VAL* 2.9 35.5 + - + +
405H LYS 3.6 4.7 - - - -
406H ILE* 3.7 19.3 - - + -
415H VAL* 4.9 5.2 - - + -
417H GLY* 1.3 72.8 - - - -
419H HIS* 1.3 63.2 + - - +
420H ILE* 5.0 5.2 - - + -
429H VAL* 5.0 0.7 - - + +
432H ALA* 3.7 30.3 - - + -
436H LEU* 5.7 0.2 - - + -
459H PHE* 3.9 5.8 - - + -
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Residues in contact with HIS 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ASP* 3.6 22.8 + - + +
222H ILE* 3.6 25.6 - - + +
365H ALA 3.7 2.9 - - - -
366H TRP* 3.3 34.4 - + + +
367H VAL 4.8 2.5 - - - -
368H GLY 4.9 0.2 - - - -
369H LYS 2.7 30.1 + - - -
370H SER* 3.6 18.9 - - - -
403H MET 4.0 0.9 - - - +
404H VAL* 3.6 1.9 - - - -
405H LYS* 2.8 51.8 + - + +
406H ILE* 5.0 0.4 - - - +
407H LEU* 3.6 17.0 - - + +
417H GLY 4.0 0.2 - - - -
418H ALA* 1.3 83.0 + - - +
420H ILE* 1.3 65.0 + - - +
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Residues in contact with ILE 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H ILE* 4.6 2.3 - - - +
364H VAL* 3.2 9.6 - - - +
365H ALA 2.7 44.3 + - - +
388H PHE* 4.0 18.6 - - + -
403H MET 3.8 1.3 - - - -
404H VAL* 4.1 13.7 - - + -
418H ALA* 5.1 3.1 - - + +
419H HIS* 1.3 82.9 - - - +
421H LEU* 1.3 62.4 + - - +
425H ALA* 3.6 26.8 - - + +
428H MET* 4.0 29.6 - - + +
429H VAL* 3.9 36.8 - - + +
459H PHE* 4.8 9.4 - - + -
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Residues in contact with LEU 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H ILE* 4.1 20.1 - - + +
225H ASN* 3.6 32.5 - - + +
226H PHE* 3.7 27.6 - - + +
229H ILE* 3.8 16.6 - - + -
362H PRO* 4.0 10.1 - - + -
363H GLU 3.6 4.5 - - - +
364H VAL* 3.7 27.6 - - + -
388H PHE* 3.4 4.8 - - - -
402H GLY* 3.1 14.4 - - - -
403H MET* 2.8 42.2 + - + +
420H ILE* 1.3 74.3 - - - +
422H GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H PRO* 3.7 12.5 - - - +
363H GLU* 2.8 30.7 + - - +
388H PHE* 3.9 3.1 - - - -
401H ASP 3.6 6.5 - - - -
420H ILE 4.0 0.8 - - - -
421H LEU* 1.3 77.2 - - - +
423H PRO* 1.3 77.3 - - - +
424H GLY 3.5 0.3 + - - -
425H ALA* 3.5 11.3 + - - +
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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