Contacts of the strand formed by residues 473 - 480 (chain A) in PDB entry 4TZ1
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 LEU 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A PRO* 4.7 11.2 - - + -
262A VAL* 3.1 54.1 - - + +
437A ASP 5.9 0.2 - - - +
438A THR 3.0 9.0 + - - +
439A ILE* 3.4 12.1 - - + +
440A ILE* 2.7 32.6 + - - +
471A ASN 3.8 3.5 + - - +
472A VAL* 1.3 76.2 - - - +
474A ALA* 1.3 55.1 + - - +
475A THR* 3.8 26.0 - - + -
495A LYS* 3.3 30.7 - - + +
497A ILE* 4.5 12.3 - - + -
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Residues in contact with ALA 474 (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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440A ILE* 3.2 18.2 - - + +
467A VAL* 6.4 0.2 - - + -
472A VAL* 4.2 0.6 - - + -
473A LEU* 1.3 72.9 - - - +
475A THR* 1.3 62.9 + - - +
476A GLY 4.1 0.7 - - - -
477A LEU* 4.0 27.4 - - + -
489A TRP* 4.3 8.4 - - + -
495A LYS 2.9 9.1 + - - +
496A THR* 3.3 19.2 - - - +
497A ILE 2.8 27.5 + - - +
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Residues in contact with THR 475 (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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201A TYR* 4.1 0.5 - - - -
220A TYR* 3.3 27.2 - - - +
222A ARG* 4.2 3.4 + - - -
260A THR* 4.1 14.1 - - + -
262A VAL 5.0 0.4 - - - +
263A SER* 6.1 0.2 - - - -
439A ILE* 5.0 1.8 - - + +
440A ILE 2.8 8.9 + - - -
441A ASP* 2.7 36.4 + - - +
442A HIS 2.9 22.9 + - - -
473A LEU* 3.8 30.5 - - + -
474A ALA* 1.3 76.4 - - - +
476A GLY* 1.3 60.1 + - - +
497A ILE* 3.4 12.3 - - + -
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Residues in contact with GLY 476 (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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201A TYR* 4.6 2.7 - - - -
220A TYR* 3.7 19.3 - - - -
440A ILE 5.5 0.4 - - - -
442A HIS* 3.3 6.7 + - - -
443A THR* 3.2 24.3 + - - +
475A THR* 1.3 72.6 - - - +
477A LEU* 1.3 60.1 + - - +
478A PHE* 3.4 16.3 - - - -
497A ILE 3.0 12.5 + - - -
498A PHE* 3.8 11.6 + - - -
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Residues in contact with LEU 477 (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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440A ILE* 4.7 3.8 - - + -
443A THR* 3.3 28.7 - - + -
465A VAL* 4.8 11.0 - - + -
474A ALA* 4.0 30.1 - - + -
476A GLY* 1.3 73.9 - - - +
478A PHE* 1.3 60.4 + - - +
479A VAL* 3.8 13.2 - - + -
487A VAL* 4.3 15.0 - - + -
489A TRP* 4.7 4.3 - - + -
496A THR* 4.1 13.2 - - + +
498A PHE* 3.0 15.0 + - - +
499A TYR* 3.2 29.2 - - + -
500A GLN 3.0 23.4 + - - -
524A TYR* 4.4 5.8 - - + -
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Residues in contact with PHE 478 (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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174A GLN* 3.9 16.4 - - + -
199A GLY 3.6 21.8 - - - -
200A GLY* 3.5 29.2 - - - -
201A TYR* 4.8 1.8 - + + -
220A TYR* 5.1 0.4 - - + -
442A HIS* 3.7 21.3 - + - -
443A THR* 3.1 16.2 + - - +
444A TRP* 3.2 22.2 - - + -
445A VAL 2.9 22.5 + - - -
476A GLY* 3.4 23.1 - - - -
477A LEU* 1.3 73.9 - - - +
479A VAL* 1.3 64.0 + - - +
498A PHE* 3.2 29.6 - + - -
500A GLN* 3.3 29.6 - - + +
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Residues in contact with VAL 479 (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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445A VAL* 3.3 26.0 - - + +
464A GLY* 4.2 1.1 - - - -
465A VAL* 4.1 9.6 - - + -
477A LEU* 3.8 20.2 - - + -
478A PHE* 1.3 79.6 - - - +
480A GLU* 1.3 63.2 + - - +
482A PHE* 3.5 18.6 - - + -
486A ASP* 3.8 18.6 - - + +
487A VAL* 3.7 19.3 - - + -
499A TYR* 4.0 12.1 - - + +
500A GLN 3.0 7.5 + - - -
501A ASN* 2.9 32.4 + - - +
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Residues in contact with GLU 480 (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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174A GLN* 3.8 2.5 + - - -
444A TRP* 2.9 27.5 + - - +
445A VAL 3.0 7.7 + - - -
446A TRP* 3.4 5.5 - - + -
447A ARG 3.0 27.4 + - - -
479A VAL* 1.3 82.8 - - - +
481A HIS* 1.3 74.7 + - + +
482A PHE* 3.3 10.0 - - - -
500A GLN* 2.8 31.5 + - - +
501A ASN* 4.1 0.7 - - - +
502A ALA* 3.4 18.5 - - - +
3B BGC 2.6 47.4 + - - -
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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