Contacts of the strand formed by residues 403 - 409 (chain D) 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 MET 403 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221D GLU* 4.0 22.9 - - + +
222D ILE* 3.7 27.5 - - + +
225D ASN* 4.4 11.7 - - - +
385D LYS* 3.8 30.5 - - + -
386D PHE 3.3 16.8 - - - +
387D PRO* 3.9 6.5 - - + -
388D PHE* 3.8 6.4 - - - -
402D GLY* 1.3 77.6 - - - +
404D VAL* 1.3 65.2 + - - +
405D LYS* 3.8 18.2 - - + -
419D HIS 3.8 0.9 - - - +
420D ILE* 3.5 1.2 - - - -
421D LEU* 2.7 41.4 + - + +
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Residues in contact with VAL 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D LYS* 3.3 6.4 - - - +
386D PHE 3.0 28.3 + - - +
388D PHE* 3.8 22.9 - - + -
403D MET* 1.3 80.0 - - - +
405D LYS* 1.3 61.2 + - - +
406D ILE* 4.2 8.1 - - + -
419D HIS 3.4 8.1 - - - +
420D ILE* 4.0 9.9 - - + -
428D MET* 4.0 13.0 - - - -
458D ALA* 3.8 29.4 - - + +
459D PHE* 4.0 24.9 - - + -
462D ALA* 3.5 15.0 - - + +
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Residues in contact with LYS 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 2.6 38.0 + - - -
221D GLU* 2.6 33.9 + - - +
222D ILE* 4.6 3.1 - - - -
371D GLU* 2.8 20.9 + - - +
383D VAL* 3.9 26.2 - - + -
384D GLY 3.4 2.9 - - - +
385D LYS* 4.1 4.5 - - + -
403D MET* 3.8 20.4 - - + -
404D VAL* 1.3 73.5 - - - +
406D ILE* 1.3 64.8 + - - +
407D LEU* 4.1 13.2 - - + -
417D GLY 3.9 0.5 - - - +
418D ALA* 3.5 4.0 - - - -
419D HIS* 2.7 52.6 + - + +
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Residues in contact with ILE 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LYS 3.7 0.5 - - - +
383D VAL* 3.4 5.5 - - - +
384D GLY 2.7 37.2 + - - +
404D VAL* 4.2 2.7 - - + -
405D LYS* 1.3 80.8 - - - +
407D LEU* 1.3 67.9 + - - +
408D GLY 4.1 0.2 + - - -
415D VAL* 4.4 6.1 - - + -
417D GLY 3.6 3.4 - - - +
418D ALA* 3.9 14.4 - - + -
442D CYS* 3.9 19.7 - - - -
459D PHE* 3.7 21.1 - - + -
462D ALA* 3.7 28.9 - - + +
463D ASN* 3.4 41.3 - - - +
466D ALA* 4.1 5.1 - - + +
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 5.0 0.7 - - - +
369D LYS 3.3 25.8 - - - +
370D SER 3.7 1.1 - - - -
371D GLU* 3.6 43.7 - - + +
374D LEU* 3.9 20.6 - - + -
381D TYR* 4.3 4.0 - - + -
382D LYS 3.4 2.7 - - - +
383D VAL* 3.7 23.1 - - + -
405D LYS* 4.1 11.9 - - + -
406D ILE* 1.3 80.5 - - - +
408D GLY* 1.3 51.2 + - - +
415D VAL* 3.6 2.4 - - - +
416D LEU* 2.6 33.7 + - - -
417D GLY 2.9 18.8 + - - +
419D HIS* 3.9 13.2 - - + +
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Residues in contact with GLY 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D TYR* 3.2 6.0 - - - -
382D LYS* 2.7 47.0 + - - +
406D ILE 4.1 1.2 - - - -
407D LEU* 1.3 74.6 - - - +
409D GLN* 1.3 63.5 + - - -
414D ARG 3.2 9.6 - - - -
416D LEU* 4.2 1.1 - - - -
442D CYS* 4.0 19.5 - - - -
466D ALA* 5.2 0.6 - - - +
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Residues in contact with GLN 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ILE* 4.3 1.6 - - + -
380D GLU* 2.7 27.8 + - - +
382D LYS* 3.8 2.4 - - - -
408D GLY* 1.3 71.4 - - - -
410D LYS* 1.3 72.7 + - - +
411D SER* 2.6 37.7 + - - +
412D THR* 3.0 29.5 + - + +
413D ASP* 3.0 22.2 + - - -
414D ARG* 2.8 16.4 + - + +
416D LEU* 3.7 25.2 - - + +
2013D SO4 2.9 35.8 + - - +
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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