Contacts of the strand formed by residues 466 - 474 (chain A) in PDB entry 3TQI
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 GLY 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LYS* 3.6 15.5 - - - +
455A SER 2.7 34.5 + - - -
465A TYR* 1.3 76.5 - - - +
467A TYR* 1.3 59.4 + - - -
505A GLU* 4.3 8.5 - - - -
506A VAL 2.6 23.4 - - - +
507A SER* 3.0 6.6 + - - +
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Residues in contact with TYR 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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418A GLU* 3.8 10.9 + - - -
419A TYR* 3.7 31.5 + + - -
422A ILE* 4.2 9.2 - - + -
450A PHE* 3.5 36.3 - + + -
451A MET 4.0 0.7 - - - +
452A PRO* 3.8 28.7 - - + -
453A LEU 4.2 0.7 - - - -
454A LYS* 3.8 34.7 - - + +
466A GLY* 1.3 72.8 - - - -
468A ILE* 1.3 61.3 + - - +
469A ILE* 6.2 0.2 - - + -
505A GLU* 3.5 24.4 + - + +
506A VAL* 2.4 36.1 + - + +
507A SER 3.0 6.1 - - - +
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Residues in contact with ILE 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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450A PHE* 4.0 2.3 - - - -
451A MET* 3.0 50.3 + - + +
453A LEU* 4.3 10.1 - - + -
454A LYS 3.9 15.9 - - - +
455A SER* 4.3 12.1 - - - +
466A GLY 4.4 1.1 - - - +
467A TYR* 1.3 80.5 - - - +
469A ILE* 1.3 72.5 + - - +
507A SER 5.0 0.2 - - - +
508A ARG* 3.7 25.8 - - + +
510A VAL* 4.4 9.0 - - + -
412B LEU* 4.0 16.8 - - + -
451B MET* 4.7 5.6 - - - -
523B TRP* 3.7 30.1 - - + -
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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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422A ILE* 5.0 2.0 - - + +
423A LEU* 4.5 9.2 - - + -
426A ALA* 4.0 25.8 - - + -
448A ALA* 4.1 7.4 - - + -
449A VAL 3.4 14.8 - - - +
450A PHE* 4.0 27.8 - - + -
451A MET* 4.5 0.7 - - - -
467A TYR 5.6 0.2 - - - -
468A ILE* 1.3 76.6 - - - +
470A ALA* 1.3 64.0 + - - +
471A LEU* 4.1 10.5 - - + -
499A ILE* 4.4 4.0 - - + -
506A VAL* 4.4 23.1 - - + -
508A ARG 3.5 5.6 + - - +
509A VAL* 3.0 26.2 - - + +
510A VAL* 2.7 35.1 + - - +
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Residues in contact with ALA 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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447A PHE 4.1 0.2 - - - +
448A ALA* 3.3 4.0 - - - -
449A VAL* 2.7 59.2 + - + +
451A MET* 3.4 15.1 - - + +
469A ILE* 1.3 74.5 - - - +
471A LEU* 1.3 62.1 + - - +
472A ARG 4.1 0.2 + - - -
510A VAL* 3.2 10.5 - - + +
512A ASP 5.6 0.2 - - - +
523A TRP* 3.4 25.6 - - + -
510B VAL* 5.0 1.1 - - + -
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Residues in contact with LEU 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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430A PHE* 3.7 37.0 - - + -
447A PHE 3.6 0.2 - - - -
448A ALA* 3.8 16.8 - - + -
469A ILE* 4.1 8.3 - - + -
470A ALA* 1.3 80.6 - - - +
472A ARG* 1.3 59.6 + - - +
492A LEU* 5.4 2.0 - - + -
495A VAL* 3.8 28.3 - - + -
499A ILE* 4.2 12.1 - - + -
509A VAL* 3.9 11.7 - - + -
510A VAL 2.6 13.4 + - - +
511A TYR* 3.5 17.8 - - + -
512A ASP* 2.9 28.7 + - - +
513B MET* 4.0 18.8 - - + -
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Residues in contact with ARG 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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430A PHE* 3.8 2.1 - - - -
445A GLN* 5.8 0.4 - - + -
446A ALA* 3.2 2.6 - - - -
447A PHE* 2.8 81.1 + - + +
449A VAL* 5.3 2.0 - - + -
470A ALA 4.1 0.2 + - - -
471A LEU* 1.3 74.7 - - - +
473A ALA* 1.3 66.3 + - - +
474A VAL* 3.8 25.0 - - + +
484A TRP* 4.1 4.9 - - - +
512A ASP* 3.1 42.2 + - - +
514A THR 2.8 32.9 + - - +
515A ASN 4.6 2.6 + - - -
516A LYS* 5.3 0.6 - - - +
519A ALA* 4.6 4.2 + - - +
520A THR 3.2 23.4 + - - -
521A ILE* 3.1 19.0 + - + +
523A TRP* 4.4 7.6 - - + +
508B ARG* 3.6 5.3 - - - +
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Residues in contact with ALA 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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430A PHE* 4.4 12.6 - - + -
434A LEU* 6.3 0.4 - - + -
443A VAL* 4.8 4.9 - - + -
445A GLN 3.2 12.6 - - - +
446A ALA* 4.1 10.5 - - + -
471A LEU 4.3 0.2 - - - -
472A ARG* 1.3 79.9 - - - +
474A VAL* 1.3 66.2 + - - +
484A TRP* 3.5 5.2 - - - +
485A ALA* 2.9 29.4 + - + -
487A LEU* 4.4 5.8 - - + -
511A TYR* 3.9 21.8 + - + +
512A ASP 5.3 1.2 + - - +
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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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443A VAL* 3.5 8.5 - - - +
444A SER* 2.8 32.5 + - - -
445A GLN* 3.1 21.0 + - + +
472A ARG* 3.8 36.6 - - + +
473A ALA* 1.3 79.7 - - - +
475A LYS* 1.3 59.4 + - - +
483A GLN* 3.5 19.7 - - + +
484A TRP* 4.3 7.0 - - - +
485A ALA* 4.1 2.5 - - - +
514A THR 5.2 0.4 - - - +
516A LYS 6.2 0.4 - - - +
521A ILE* 3.5 34.1 - - + -
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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