Contacts of the strand formed by residues 463 - 469 (chain A) in PDB entry 3H11
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 TYR 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLN* 3.6 26.9 - - - -
360A TYR* 4.8 3.0 + - - -
406A CYS* 3.7 15.3 - - - -
407A THR 3.8 3.4 - - - -
408A ALA* 4.0 13.2 - - + -
412A LEU* 3.6 20.5 - - + +
419A SER* 4.7 7.3 + - - -
420A PRO 3.7 8.8 + - - -
421A SER* 3.8 4.4 - - - -
422A LEU* 3.4 41.3 + - + +
423A TYR* 4.1 5.4 - - + -
450A MET* 4.0 26.0 - - + +
453A TRP* 3.9 20.4 - + - -
454A ASN* 2.8 30.6 + - - +
461A GLU 3.8 14.1 - - - -
462A LYS* 1.3 76.1 - - - +
464A TYR* 1.3 62.0 + - - +
465A VAL 3.9 0.9 + - - -
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Residues in contact with TYR 464 (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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405A LEU 3.8 0.7 - - - +
406A CYS* 3.1 7.3 - - - -
407A THR* 2.9 56.6 + - - +
408A ALA* 5.5 0.9 - - - -
454A ASN* 4.7 5.8 - - - +
459A ALA* 4.0 21.1 - - + +
462A LYS* 3.5 39.9 - - + +
463A TYR* 1.3 74.7 - - - +
465A VAL* 1.3 60.5 + - - +
466A TRP 4.3 0.4 - - - -
380B ASP* 3.7 35.9 - - + +
381B GLU* 4.1 16.2 - - + -
382B ALA 5.5 0.2 - - - -
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Residues in contact with VAL 465 (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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404A SER* 4.5 3.4 - - - +
405A LEU 3.6 4.7 - - - +
406A CYS* 4.2 11.9 - - - -
423A TYR* 4.4 8.7 - - + -
443A HIS* 3.5 20.4 - - + -
446A LEU* 4.6 0.2 - - + -
447A ASN* 3.1 33.8 + - + +
450A MET* 3.8 31.2 - - + -
463A TYR 3.9 4.0 + - - +
464A TYR* 1.3 78.9 - - - +
466A TRP* 1.3 66.7 + - - +
467A LEU* 4.5 1.8 - - + -
380B ASP* 4.2 4.4 + - - +
454B THR* 3.4 26.3 - - - +
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Residues in contact with TRP 466 (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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333A LEU* 6.2 1.6 - - + -
403A TRP* 4.5 11.7 - + + -
405A LEU* 2.8 57.6 + - + +
465A VAL* 1.3 74.3 - - - +
467A LEU* 1.3 67.6 + - - +
468A GLN* 3.5 42.6 - - + -
376B ARG* 3.0 67.3 + - + +
378B ILE* 3.7 22.8 + - + +
379B PRO 4.3 2.2 - - - -
380B ASP* 3.5 18.2 - - - +
452B THR* 3.4 25.2 - - + +
453B PHE 3.8 2.7 - - - -
454B THR* 3.9 6.1 - - + -
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Residues in contact with LEU 467 (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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402A PHE* 4.0 7.6 - - + -
403A TRP 3.3 13.7 - - - +
404A SER* 3.6 7.6 - - - -
440A LEU* 4.0 13.2 - - + -
443A HIS* 3.6 39.3 - - + +
444A ILE* 4.3 2.0 - - + -
447A ASN* 3.8 24.0 - - - +
465A VAL* 4.5 1.1 - - + -
466A TRP* 1.3 85.2 - - - +
468A GLN* 1.3 62.1 + - - +
452B THR* 3.2 6.6 - - - +
453B PHE* 2.8 74.2 + - + +
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Residues in contact with GLN 468 (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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337A ARG* 2.8 24.3 + - - +
402A PHE* 5.0 0.4 - - - -
403A TRP* 2.8 38.3 + - + +
466A TRP* 3.5 34.9 - - + -
467A LEU* 1.3 77.0 - - - +
469A HIS* 1.3 62.6 + - - +
375B THR 5.4 1.8 + - - -
377B TYR* 3.9 15.4 - - - -
450B GLN* 3.3 33.3 + - + +
451B PRO 3.3 6.1 - - - +
452B THR* 2.8 25.2 + - - +
453B PHE* 5.0 0.7 - - - -
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Residues in contact with HIS 469 (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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401A PHE 3.2 15.3 - - - +
402A PHE* 3.9 20.4 - + + -
403A TRP* 4.9 1.8 - - - -
440A LEU* 3.8 20.1 - - + +
468A GLN* 1.3 79.4 - - - +
470A THR* 1.3 63.6 + - - +
471A LEU* 3.0 27.7 + - + +
425B LEU* 5.3 2.2 + - - +
429B THR* 3.6 21.9 + - - -
432B ASN* 3.8 16.6 - - - -
450B GLN* 3.4 10.7 - - - +
451B PRO* 3.2 44.8 + - + +
453B PHE* 3.8 27.1 - + - -
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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