Contacts of the strand formed by residues 450 - 454 (chain D) in PDB entry 4Z2C
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 GLN 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419D CYS* 3.9 9.1 - - - +
428D GLU* 3.1 27.6 + - - +
430D PHE* 3.5 14.4 - - + -
445D ARG* 2.8 52.4 + - + +
446D ASN* 3.7 5.7 + - - +
447D ARG* 4.4 0.3 - - - -
448D GLU 3.6 1.8 - - - -
449D PHE* 1.3 108.6 - - + +
451D ALA* 1.3 61.1 + - - +
600D MET* 3.1 45.9 + - + +
602D PRO* 4.1 2.8 - - - +
605D ARG* 3.5 6.1 - - - +
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Residues in contact with ALA 451 (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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416D LEU* 4.6 1.3 - - + -
417D ALA 3.3 15.9 - - - +
418D ASP* 3.7 2.9 - - - -
419D CYS* 3.6 17.2 - - + +
428D GLU 2.9 7.8 + - - +
429D LEU* 3.5 10.0 - - + -
430D PHE* 2.9 25.1 + - - +
445D ARG* 4.4 0.7 - - - +
450D GLN* 1.3 74.4 - - - +
452D ILE* 1.3 67.3 + - - +
498D TYR* 3.6 26.7 - - + +
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Residues in contact with ILE 452 (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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416D LEU* 3.3 10.5 - - - +
417D ALA* 3.2 29.8 + - + +
429D LEU* 4.4 0.2 - - - -
430D PHE* 3.6 26.9 - - + +
432D VAL* 4.1 17.9 - - + -
438D GLY* 4.8 6.3 - - - +
441D ALA* 4.0 21.3 - - + +
442D LYS* 4.0 18.2 - - + +
445D ARG* 3.7 22.2 - - + -
450D GLN 5.1 0.2 - - - -
451D ALA* 1.3 85.3 - - - +
453D LEU* 1.3 65.1 + - - +
454D PRO* 3.8 4.5 - - + +
600D MET* 3.8 24.2 - - + -
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Residues in contact with LEU 453 (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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413D PRO* 5.4 3.1 - - + -
415D LYS* 4.6 4.3 - - + -
416D LEU* 3.7 33.9 - - + +
429D LEU* 3.7 23.6 - - + -
430D PHE 2.9 9.7 + - - -
431D ILE* 3.4 12.5 - - + +
432D VAL 2.9 25.0 + - - +
451D ALA 4.3 0.2 + - - -
452D ILE* 1.3 75.8 - - - +
454D PRO* 1.3 87.8 - - + +
455D ILE* 3.8 1.1 + - + -
478D SER* 4.1 24.5 - - - +
479D LEU* 4.3 24.9 - - + +
482D ALA* 4.5 7.2 - - + -
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Residues in contact with PRO 454 (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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415D LYS* 4.0 16.5 - - + +
416D LEU* 4.0 9.0 - - - +
432D VAL* 3.1 10.8 - - + +
434D GLY* 4.4 21.1 - - - +
435D ASP* 4.8 6.3 - - + +
438D GLY* 5.0 10.5 - - - -
452D ILE* 3.8 8.7 - - + +
453D LEU* 1.3 114.6 - - + +
455D ILE* 1.3 58.3 + - - +
456D ARG* 3.8 3.8 - - + +
475D GLU* 4.0 7.8 - - - +
478D SER* 5.1 0.3 + - - -
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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