Contacts of the strand formed by residues 475 - 478 (chain D) in PDB entry 1Z10
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 PRO 475 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D TYR* 3.3 15.7 - - - +
362D PHE* 6.1 1.3 - - + -
400D ARG* 6.1 2.9 - - - +
473D VAL 4.0 0.2 - - - +
474D SER* 1.3 91.3 + - - +
476D LYS* 1.3 65.0 + - - +
477D HIS 3.8 1.3 - - - +
478D VAL* 3.5 33.4 - - + +
482D THR* 3.7 17.7 - - + -
483D ILE 3.5 12.1 - - - +
484D PRO* 4.6 1.6 - - + -
485D ARG* 3.5 13.9 + - - -
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Residues in contact with LYS 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D GLN* 2.8 34.6 + - - +
474D SER 3.8 1.2 + - - -
475D PRO* 1.3 75.7 - - - +
477D HIS* 1.3 87.0 + - + +
483D ILE 2.7 15.8 + - - +
484D PRO 3.8 4.7 - - - +
485D ARG* 3.6 32.3 - - + +
486D ASN* 3.1 34.9 + - - +
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Residues in contact with HIS 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU 6.0 0.4 - - - -
210D GLN* 3.3 39.7 + - + +
213D SER* 3.4 23.6 + - - +
214D THR* 4.0 24.1 - - + +
475D PRO* 3.8 0.5 - - - +
476D LYS* 1.3 117.0 + - + +
478D VAL* 1.3 67.4 + - - +
481D ALA 4.3 0.9 - - - -
483D ILE* 2.8 36.9 + - + +
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Residues in contact with VAL 478 (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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51D THR 5.0 0.2 - - - +
52D GLU 3.7 21.2 + - - +
53D GLN* 5.7 3.6 - - - -
54D MET 4.5 6.8 + - - -
55D TYR* 4.3 22.0 - - + +
213D SER 3.4 9.2 + - - +
218D GLN* 5.0 1.7 - - - +
364D ASP* 5.7 0.2 - - - +
367D PRO* 3.9 24.2 - - + -
475D PRO* 3.5 29.2 - - + -
477D HIS* 1.3 82.6 - - - +
479D GLY* 1.3 60.1 + - - +
481D ALA 3.3 4.0 - - - -
482D THR* 3.9 10.8 - - + +
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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