Contacts of the strand formed by residues 467 - 476 (chain A) in PDB entry 3L2P
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 SER 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A LEU* 4.3 11.4 - - - -
431A LYS 3.2 11.7 - - - -
432A ASN* 4.2 13.9 - - - -
466A HIS* 1.3 82.8 + - - +
468A MET* 1.3 71.4 + - - +
512A TYR* 3.5 5.5 - - - -
513A PHE* 3.6 0.9 - - - -
514A ASN* 2.9 23.0 + - - +
515A ASP* 2.9 40.9 + - - -
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Residues in contact with MET 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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390A LEU* 4.5 0.2 - - - +
429A VAL* 5.4 0.7 - - - +
430A HIS* 3.5 0.3 - - - -
431A LYS* 3.1 51.3 + - + +
458A ILE* 4.4 6.5 - - + -
462A PHE* 3.7 36.6 - - + -
465A GLY 3.2 29.4 - - - +
467A SER* 1.3 76.6 - - - +
469A ILE* 1.3 71.6 + - - +
470A LEU* 3.2 25.6 - - + -
512A TYR* 3.1 18.5 - - - +
513A PHE* 3.6 27.8 - - + -
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Residues in contact with ILE 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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388A ALA* 6.4 1.1 - - + -
389A SER 6.1 0.7 - - - -
390A LEU* 3.2 25.1 - - + -
394A VAL* 5.0 3.4 - - + -
428A GLN* 3.9 13.7 - - + +
429A VAL 3.2 2.9 - - - +
430A HIS* 3.2 52.5 - - + +
468A MET* 1.3 83.4 - - - +
470A LEU* 1.3 62.6 + - - +
510A CYS* 3.8 2.4 - - - -
511A ILE* 2.9 43.8 + - + +
512A TYR* 2.8 38.5 + - + +
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Residues in contact with LEU 470 (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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427A VAL 4.8 0.2 - - - -
428A GLN* 3.4 8.9 - - - +
429A VAL* 2.9 55.0 + - + +
458A ILE* 5.3 6.1 - - + -
462A PHE* 3.8 31.9 - - + -
468A MET* 3.2 42.4 - - + -
469A ILE* 1.3 79.0 - - - +
471A ASP* 1.3 61.3 + - - +
472A SER* 5.4 0.4 - - - -
505A LEU* 5.4 1.3 - - + -
507A VAL* 4.0 27.4 - - + -
509A ASP 3.6 10.5 - - - +
510A CYS* 5.2 6.1 - - + -
511A ILE* 5.2 0.7 - - - -
512A TYR 5.2 0.2 - - - +
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Residues in contact with ASP 471 (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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396A PRO* 5.0 1.9 - - - +
426A ARG* 2.5 41.1 + - - +
427A VAL 4.1 2.6 - - - +
428A GLN* 4.6 9.1 - - + +
470A LEU* 1.3 73.9 - - - +
472A SER* 1.3 62.5 + - - +
507A VAL* 4.0 1.2 - - - -
508A PHE* 3.2 17.4 + - - -
509A ASP* 3.2 43.3 + - + +
511A ILE* 4.6 10.5 - - + -
579A TYR* 2.6 35.0 + - - +
586A TRP* 4.1 0.2 - - - -
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Residues in contact with SER 472 (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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426A ARG* 3.5 12.3 - - - -
427A VAL* 2.7 47.3 + - - +
429A VAL* 4.3 3.4 - - - +
470A LEU* 5.2 0.4 - - - -
471A ASP* 1.3 77.5 + - - +
473A GLU* 1.3 56.5 + - - +
505A LEU* 3.3 36.4 - - - +
506A PHE 3.3 16.8 - - - -
507A VAL* 3.8 7.9 - - - -
508A PHE* 3.3 10.3 - - - -
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Residues in contact with GLU 473 (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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422A TYR* 3.2 46.8 - - + +
424A GLY* 3.2 32.7 - - - +
425A GLU 3.5 2.5 - - - +
426A ARG* 3.4 28.2 + - - +
472A SER* 1.3 75.5 - - - +
474A VAL* 1.3 63.4 + - - +
475A LEU* 4.1 2.2 - - + -
504A CYS 3.8 0.7 - - - +
505A LEU* 3.6 4.3 - - - +
506A PHE* 2.9 35.1 + - - +
508A PHE* 3.6 7.4 - - + -
901A AMP 3.7 27.7 + - - +
11B C 5.3 2.1 - - - +
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Residues in contact with VAL 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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424A GLY* 3.6 1.6 - - - -
425A GLU* 2.9 39.8 + - + +
427A VAL* 3.8 15.7 - - + +
450A LYS* 3.8 14.4 - - + +
451A VAL* 5.3 0.4 - - + -
454A PHE* 3.7 11.7 - - + -
473A GLU* 1.3 73.0 - - - +
475A LEU* 1.3 68.3 + - - +
490A LEU* 3.6 21.3 - - + +
503A VAL* 3.6 22.4 - - + -
504A CYS 3.3 5.8 - - - +
505A LEU* 3.4 23.8 - - + -
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Residues in contact with LEU 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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422A TYR* 3.8 32.8 - - + -
423A ASP 4.6 11.7 - - - +
424A GLY* 4.2 8.5 - - - -
473A GLU* 4.1 7.9 - - + +
474A VAL* 1.3 81.8 - - - +
476A LEU* 1.3 60.0 + - - +
477A ILE* 3.7 1.9 + - + -
484A PRO* 3.5 31.2 - - + -
485A LEU 5.0 6.7 - - - +
490A LEU* 4.5 5.8 - - - -
503A VAL* 3.3 7.0 - - - +
504A CYS* 2.4 44.0 + - - +
506A PHE* 3.8 29.4 - - + -
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Residues in contact with LEU 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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475A LEU* 1.3 72.7 - - - +
477A ILE* 1.3 61.4 + - - +
484A PRO* 3.9 1.7 - - - +
485A LEU* 3.1 58.8 + - + +
489A THR* 3.6 42.4 - - + +
490A LEU* 4.3 11.6 - - + +
495A LYS* 3.8 27.1 - - + +
498A PHE* 3.9 14.1 - - + -
501A ALA* 3.8 15.9 - - + +
502A ASN* 3.7 25.8 - - - -
503A VAL* 3.9 6.1 - - + +
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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