Contacts of the helix formed by residues 488 - 503 (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 PRO 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A TYR* 3.2 38.8 - - + +
486A ASP 3.9 1.5 - - - +
487A LEU* 1.3 91.3 - - + +
489A HIS* 1.3 67.7 + - - +
490A GLU* 4.6 8.1 - - + +
491A PHE* 3.0 28.6 + - + +
492A LEU* 3.0 12.6 + - - +
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Residues in contact with HIS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU 3.6 3.0 + - - -
488A PRO* 1.3 69.3 - - - +
490A GLU* 1.3 64.4 + - + +
492A LEU* 3.0 10.9 + - - +
493A SER* 2.9 40.2 + - - -
483B GLN* 6.2 0.4 - - - -
484B TRP* 3.1 70.6 + + - -
486B ASP* 3.5 44.1 + - + +
515B ASN* 5.8 0.2 + - - -
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PRO* 3.2 8.5 + - + +
489A HIS* 1.3 85.7 - - + +
491A PHE* 1.3 66.6 + - + +
493A SER* 3.5 7.3 + - - -
494A LYS* 3.1 22.2 + - - +
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Residues in contact with PHE 491 (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* 4.7 2.9 - + - -
433A GLU* 3.6 16.8 - - + -
434A LEU* 3.6 52.0 - - + -
437A SER* 3.8 21.1 - - - -
439A TYR* 4.0 14.6 - + + -
487A LEU* 4.4 14.6 - - + -
488A PRO* 3.0 31.6 + - + +
490A GLU* 1.3 82.6 - - + +
492A LEU* 1.3 78.2 + - + +
494A LYS* 3.1 10.7 + - + +
495A VAL* 3.1 40.2 + - + +
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Residues in contact with LEU 492 (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* 5.2 6.7 - - + -
471A LEU* 5.4 1.6 - - + -
487A LEU* 3.1 53.4 - - + +
488A PRO 3.0 29.4 + - - +
489A HIS* 3.0 8.6 + - - +
491A PHE* 1.3 82.6 - - + +
493A SER* 1.3 58.1 + - - +
495A VAL* 3.0 6.1 + - + +
496A SER* 2.8 31.6 + - - -
511A TYR* 4.6 15.9 - - + -
484B TRP* 3.9 9.2 - - + -
513B MET* 3.7 36.5 - - + +
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Residues in contact with SER 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A HIS* 2.9 24.6 + - - -
490A GLU* 3.6 13.0 - - - -
492A LEU* 1.3 76.4 - - - +
494A LYS* 1.3 52.9 + - - +
496A SER* 2.8 8.8 + - - -
497A HIS* 2.7 39.9 + - - +
484B TRP* 3.0 26.1 + - - +
515B ASN* 4.7 11.3 + - - +
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Residues in contact with LYS 494 (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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433A GLU* 3.1 39.9 + - + +
436A LYS* 5.3 4.9 - - - +
437A SER* 5.2 5.3 + - - -
490A GLU 3.1 11.6 + - - +
491A PHE* 3.1 13.7 + - + +
493A SER* 1.3 79.0 - - - +
495A VAL* 1.3 60.8 + - + +
497A HIS* 4.0 5.8 - - + +
498A ARG* 3.3 31.1 + - - +
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Residues in contact with VAL 495 (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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429A ILE* 4.3 5.1 - - + +
430A PHE* 3.6 34.5 - - + -
433A GLU* 4.1 17.3 - - + -
471A LEU* 3.8 16.4 - - + -
491A PHE* 3.1 43.9 + - + +
492A LEU* 3.0 9.0 + - + +
494A LYS* 1.3 75.4 - - - +
496A SER* 1.3 63.8 + - - +
498A ARG* 3.4 4.6 + - - +
499A ILE* 3.1 32.4 + - + +
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU 2.8 16.7 + - - -
493A SER* 2.8 15.8 + - - -
495A VAL* 1.3 72.2 - - - +
497A HIS* 1.3 72.8 + - - +
498A ARG 3.3 0.2 + - - -
499A ILE* 3.4 3.5 + - - +
500A VAL* 3.2 29.8 + - - +
509A VAL* 3.2 28.0 - - - -
484B TRP* 4.6 0.2 + - - -
513B MET* 2.7 34.6 + - - +
514B THR* 4.7 4.2 - - - -
515B ASN* 5.4 2.6 + - - -
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Residues in contact with HIS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 2.7 23.6 + - - +
494A LYS* 4.0 7.2 - - + +
496A SER* 1.3 74.4 + - - +
498A ARG* 1.3 57.2 + - - +
500A VAL* 4.2 2.6 - - - +
501A ASN* 3.2 59.7 + - - +
514B THR* 6.5 0.4 - - - -
515B ASN* 4.1 19.5 + - - +
517B PRO* 5.2 6.7 - - + -
518B PRO* 4.4 27.6 - - + +
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Residues in contact with ARG 498 (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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429A ILE* 3.8 26.4 - - + +
432A GLU* 3.1 29.3 + - - -
433A GLU* 3.1 33.0 + - - -
436A LYS* 4.6 6.2 - - - +
494A LYS* 3.3 24.0 + - - +
495A VAL* 3.8 3.8 - - - +
496A SER 3.2 0.6 - - - -
497A HIS* 1.3 79.5 - - - +
499A ILE* 1.3 58.3 + - - +
501A ASN* 4.6 2.5 - - - +
502A GLU* 2.8 86.7 + - + +
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Residues in contact with ILE 499 (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 ALA* 3.9 42.6 - - + +
429A ILE* 4.0 21.1 - - + +
469A ILE* 4.4 15.5 - - + -
471A LEU* 4.2 20.4 - - + -
495A VAL* 3.1 34.7 + - + +
496A SER* 3.4 4.7 + - - +
498A ARG* 1.3 75.4 - - - +
500A VAL* 1.3 64.3 + - + +
503A ILE* 3.1 30.3 + - + +
506A VAL* 4.4 9.3 - - + +
509A VAL* 4.4 11.4 - - + -
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Residues in contact with VAL 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A SER 3.2 17.0 + - - +
497A HIS* 4.3 2.9 - - - +
499A ILE* 1.3 76.6 - - - +
501A ASN* 1.3 63.3 + - - +
503A ILE 2.9 18.8 - - - +
504A LYS* 4.5 2.3 + - - -
506A VAL* 4.3 8.1 - - + -
507A SER* 3.7 24.4 + - - +
508A ARG* 3.3 31.6 - - - +
509A VAL* 4.2 6.1 - - + +
514B THR* 4.4 9.2 - - + +
518B PRO* 4.3 26.9 - - + +
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Residues in contact with ASN 501 (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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497A HIS* 3.2 49.4 + - - +
498A ARG* 4.0 3.1 - - - +
500A VAL* 1.3 79.2 - - - +
502A GLU* 1.3 69.4 + - + +
503A ILE 4.3 2.1 - - - -
504A LYS* 4.5 2.3 + - - +
518B PRO* 4.3 16.3 - - - +
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.5 17.3 - - + +
498A ARG* 2.8 67.6 + - + +
501A ASN* 1.3 78.4 - - + +
503A ILE* 1.3 61.3 + - + +
504A LYS* 3.4 4.0 + - - +
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Residues in contact with ILE 503 (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* 3.7 13.9 - - + +
425A GLN* 3.3 33.7 - - + +
426A ALA* 3.2 42.6 - - + +
429A ILE* 4.4 8.7 - - + -
499A ILE* 3.1 20.6 + - + +
500A VAL 2.9 20.5 - - - +
502A GLU* 1.3 75.8 - - + +
504A LYS* 1.3 76.7 + - - +
505A GLU* 3.5 12.6 - - - +
506A VAL* 3.5 22.4 + - + +
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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