Contacts of the strand formed by residues 445 - 455 (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 GLN 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ARG* 4.7 3.2 - - - +
400A HIS* 3.6 16.6 + - - +
401A PRO* 3.1 41.8 + - + +
410A ARG* 4.0 4.3 - - - +
443A VAL* 3.3 3.9 + - - +
444A SER* 1.3 80.2 - - - +
446A ALA* 1.3 76.4 + - - +
447A PHE* 3.5 33.2 - - + -
472A ARG* 5.8 0.7 - - + -
473A ALA* 3.2 4.1 - - - +
474A VAL* 3.1 40.2 + - + +
521A ILE* 4.5 12.2 - - + +
522A GLU* 4.0 9.7 - - - +
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Residues in contact with ALA 446 (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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266A ARG* 3.0 17.3 + - - -
400A HIS* 3.7 20.0 - - + +
430A PHE* 4.2 5.4 - - + -
431A ILE* 4.2 6.2 - - + +
434A LEU* 4.0 27.4 - - + -
443A VAL* 4.1 5.2 - - + -
445A GLN* 1.3 85.6 + - - +
447A PHE* 1.3 63.0 + - - +
472A ARG 3.2 9.4 - - - +
473A ALA* 4.1 9.9 - - + -
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Residues in contact with PHE 447 (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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266A ARG* 3.3 4.0 - - - +
410A ARG* 3.1 50.9 - - - +
427A ASP* 3.7 5.6 - - - +
430A PHE* 3.6 13.0 - - - -
431A ILE* 5.5 0.2 - - - -
445A GLN* 3.5 31.4 - - + -
446A ALA* 1.3 75.0 - - - +
448A ALA* 1.3 59.7 + - - +
449A VAL* 3.6 26.2 - - + -
471A LEU* 3.6 2.6 - - - -
472A ARG* 2.8 67.7 + - + +
521A ILE* 3.7 15.5 - - + -
522A GLU* 3.7 19.7 - - - -
523A TRP* 4.8 4.0 - + - -
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Residues in contact with ALA 448 (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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410A ARG* 3.9 11.4 - - - +
423A LEU* 3.3 20.3 - - + +
426A ALA* 4.3 1.6 - - + -
427A ASP* 3.2 37.3 + - + +
430A PHE* 4.4 0.6 - - + -
447A PHE* 1.3 77.7 - - - +
449A VAL* 1.3 66.6 + - - +
469A ILE* 4.1 9.9 - - + -
470A ALA 3.3 4.7 - - - +
471A LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 449 (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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410A ARG* 3.2 24.5 - - - +
412A LEU* 5.7 2.5 - - + -
423A LEU* 3.8 3.1 - - - -
447A PHE* 3.6 26.0 - - + -
448A ALA* 1.3 77.7 - - - +
450A PHE* 1.3 60.1 + - - +
451A MET* 4.9 3.1 - - + -
469A ILE* 3.4 7.8 - - - +
470A ALA* 2.7 66.6 + - + +
472A ARG* 5.3 1.1 - - + -
523A TRP* 3.8 39.5 - - + +
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Residues in contact with PHE 450 (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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410A ARG 2.8 13.9 + - - +
411A ILE* 4.2 12.6 - - + -
412A LEU* 3.2 25.0 + - - +
419A TYR* 3.4 51.8 - + + -
422A ILE* 3.5 31.4 - - + -
423A LEU* 3.8 17.2 - - + +
449A VAL* 1.3 73.5 - - - +
451A MET* 1.3 61.4 + - - +
452A PRO* 3.9 19.1 - - + +
467A TYR* 3.5 36.3 - + + -
468A ILE 4.0 2.2 - - - -
469A ILE* 4.0 16.8 - - + -
506A VAL* 6.0 1.8 - - + -
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Residues in contact with MET 451 (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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412A LEU* 3.9 13.5 - - + -
449A VAL* 4.9 0.9 - - + -
450A PHE* 1.3 75.4 - - - +
452A PRO* 1.3 62.0 - - - +
453A LEU* 3.0 12.3 + - + +
467A TYR* 4.0 5.4 - - - +
468A ILE* 3.0 40.4 + - + +
470A ALA* 3.4 21.1 - - + +
510A VAL* 3.3 34.5 - - + -
523A TRP* 4.0 20.4 - - + -
451B MET* 3.8 31.4 - - + +
453B LEU* 3.8 16.4 - - + -
468B ILE* 4.6 4.5 - - + -
510B VAL* 4.8 1.6 - - + -
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Residues in contact with PRO 452 (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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411A ILE* 5.7 0.7 - - + -
412A LEU* 4.2 1.3 - - + -
413A GLY* 4.1 28.3 - - - +
419A TYR* 4.2 21.1 - - + +
450A PHE* 3.9 21.5 - - + +
451A MET* 1.3 81.0 - - - +
453A LEU* 1.3 60.7 + - - +
454A LYS 3.9 0.7 - - - -
467A TYR* 3.8 18.2 - - + -
453B LEU* 3.7 22.2 - - + -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A MET* 3.0 6.7 + - + +
452A PRO* 1.3 79.5 - - - +
454A LYS* 1.3 76.9 + - - +
468A ILE* 4.3 7.6 - - + -
412B LEU* 3.6 27.5 - - + +
413B GLY* 5.1 3.6 - - - +
451B MET* 3.6 31.4 - - + -
452B PRO* 3.6 24.0 - - + -
453B LEU* 3.3 38.4 - - + -
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Residues in contact with LYS 454 (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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452A PRO 3.9 0.6 - - - -
453A LEU* 1.3 91.2 - - - +
455A SER* 1.3 61.4 + - - +
465A TYR* 4.1 21.9 + - + +
466A GLY* 3.1 36.6 - - - +
467A TYR* 3.8 40.2 - - + +
468A ILE* 3.9 10.5 - - - +
412B LEU* 4.0 14.4 - - - +
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Residues in contact with SER 455 (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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454A LYS* 1.3 75.5 - - - +
456A VAL* 1.3 62.0 + - - +
465A TYR* 3.1 5.6 - - - -
466A GLY 2.7 29.7 + - - -
468A ILE* 4.3 13.1 - - - +
507A SER* 3.1 16.3 + - - -
508A ARG* 2.9 34.9 + - - +
412B LEU* 4.8 1.1 - - - -
523B TRP* 4.5 20.4 - - - -
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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