Contacts of the helix formed by residues 494 - 510 (chain A) in PDB entry 2PTM
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 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A LYS 3.5 4.2 - - - +
493A LEU* 1.3 92.1 - - + +
495A SER* 1.3 64.6 + - - +
496A HIS* 3.1 35.4 - - + +
497A LEU* 3.0 18.9 + - + -
498A ARG* 3.0 18.4 + - - +
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Residues in contact with SER 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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493A LEU 3.7 1.4 + - - -
494A PRO* 1.3 71.8 - - - +
496A HIS* 1.3 58.1 + - - +
498A ARG* 3.3 11.2 + - - +
499A ASN* 2.9 45.6 + - - -
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Residues in contact with HIS 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A PRO* 3.1 37.8 - - + +
495A SER* 1.3 83.5 + - - +
497A LEU* 1.3 81.6 + - + +
499A ASN* 3.9 7.1 - - - +
500A LYS* 3.1 24.6 + - - +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 4.3 18.4 - - + -
494A PRO* 3.0 25.8 + - + +
496A HIS* 1.3 96.6 - - + +
498A ARG* 1.3 65.4 + - - +
499A ASN 3.2 1.1 - - - -
500A LYS* 3.2 19.0 + - + +
501A ILE* 3.0 47.8 + - + +
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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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485A GLU 4.9 2.4 + - - -
488A MET* 3.2 52.9 + - + +
489A GLN* 3.1 36.4 + - - +
492A LYS* 3.6 19.4 - - - +
493A LEU* 2.9 25.3 + - + +
494A PRO 3.0 16.3 + - - +
495A SER* 3.6 11.2 - - - +
497A LEU* 1.3 75.0 - - - +
499A ASN* 1.3 61.3 + - - +
501A ILE* 3.3 3.3 + - - +
502A LEU* 3.0 36.3 + - + +
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Residues in contact with ASN 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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301A NCO 5.3 8.0 + - - +
495A SER* 2.9 32.0 + - - +
496A HIS* 3.9 6.1 - - - +
498A ARG* 1.3 78.2 - - - +
500A LYS* 1.3 58.7 + - - +
502A LEU* 3.9 13.1 - - - +
503A ASP* 2.9 43.5 + - - +
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Residues in contact with LYS 500 (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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496A HIS 3.1 16.2 + - - +
497A LEU* 3.2 24.3 + - + +
499A ASN* 1.3 76.3 - - - +
501A ILE* 1.3 58.9 + - + +
503A ASP* 4.5 2.9 - - - -
504A TYR* 2.9 24.8 + - - +
567A GLN* 3.0 43.8 + - - +
568A PRO 5.7 1.6 - - - -
570A ASP* 3.0 28.9 + - - -
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Residues in contact with ILE 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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484A VAL* 4.0 9.4 - - + -
487A TYR* 6.2 1.3 - - + -
488A MET* 3.7 26.2 - - + -
493A LEU* 3.9 17.5 - - + -
497A LEU* 3.0 30.1 + - + +
498A ARG 3.6 4.0 - - - +
499A ASN 3.3 0.2 - - - -
500A LYS* 1.3 76.1 - - + +
502A LEU* 1.3 65.6 + - - +
504A TYR* 3.1 7.5 + - + +
505A TYR* 3.0 45.8 + - + -
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Residues in contact with LEU 502 (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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301A NCO 4.2 13.5 + - - +
477A TYR* 5.0 0.3 + - - -
481A LEU* 4.1 23.8 - - + +
484A VAL* 4.5 4.9 - - + -
485A GLU* 3.9 38.1 - - + +
488A MET* 4.0 18.6 - - + -
498A ARG* 3.0 22.6 + - + +
499A ASN* 4.0 16.2 - - - +
501A ILE* 1.3 74.4 - - - +
503A ASP* 1.3 66.4 + - - +
505A TYR* 3.3 5.6 + - - +
506A GLU* 3.0 24.1 + - - +
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Residues in contact with ASP 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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301A NCO 3.0 43.6 + - - -
499A ASN* 2.9 31.1 + - - +
500A LYS* 3.6 5.9 - - - +
502A LEU* 1.3 75.9 - - - +
504A TYR* 1.3 57.6 + - - +
506A GLU* 3.8 3.3 - - - +
507A TYR* 2.9 31.7 + - - +
567A GLN* 3.9 2.0 - - - +
629A TYR* 3.5 19.3 + - - +
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Residues in contact with TYR 504 (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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500A LYS 2.9 14.9 + - - +
501A ILE* 3.1 11.8 + - + +
503A ASP* 1.3 74.3 - - - +
505A TYR* 1.3 77.6 + + - +
507A TYR* 3.8 4.5 - - - +
508A ARG* 2.8 74.7 + - + +
509A TYR* 4.5 8.7 - + - -
565A VAL* 3.3 45.6 + - + +
566A PHE* 5.5 0.4 - - - -
567A GLN* 3.5 25.5 - - + +
629A TYR* 5.0 0.4 - - - -
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Residues in contact with TYR 505 (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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477A TYR* 3.7 9.8 - + + +
480A LYS* 3.9 30.0 + - + +
481A LEU* 3.8 30.3 - - + -
484A VAL* 3.7 24.4 - - + +
501A ILE* 3.0 43.8 + - + -
502A LEU* 3.3 4.0 + - - +
504A TYR* 1.3 86.6 - + - +
506A GLU* 1.3 58.5 + - - +
509A TYR* 2.9 64.7 + + - +
510A ARG 3.7 0.7 + - - -
513A MET* 4.5 4.0 - - + -
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Residues in contact with GLU 506 (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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301A NCO 2.9 57.0 + - - +
477A TYR* 3.6 16.0 + - - +
502A LEU 3.0 16.8 + - - +
503A ASP* 3.8 4.6 - - - +
505A TYR* 1.3 77.9 - - - +
507A TYR* 1.3 58.3 + - - +
510A ARG* 2.9 43.5 + - - +
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Residues in contact with TYR 507 (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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503A ASP 2.9 19.0 + - - +
504A TYR 3.8 2.5 - - - +
506A GLU* 1.3 79.3 + - - +
508A ARG* 1.3 65.5 + - - +
510A ARG* 3.0 46.3 + - - +
565A VAL* 4.0 13.7 - - + -
587A GLN* 6.0 1.4 - - - +
629A TYR* 3.4 64.7 + + + +
631A THR* 4.2 26.7 - - + +
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Residues in contact with ARG 508 (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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504A TYR* 2.8 49.7 + - + +
507A TYR* 1.3 85.4 - - - +
509A TYR* 1.3 103.3 + - + +
510A ARG* 4.5 2.4 - - - +
563A PHE* 3.9 44.9 + - + +
564A GLU* 5.4 0.8 - - - +
565A VAL* 4.1 24.4 - - + +
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Residues in contact with TYR 509 (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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477A TYR* 3.8 13.7 - - + -
504A TYR* 4.5 7.0 - + - -
505A TYR* 2.9 50.4 + + - +
508A ARG* 1.3 127.4 + - + +
510A ARG* 1.3 73.1 + - - +
511A GLY 3.1 0.2 - - - -
512A LYS* 3.0 31.4 + - - +
513A MET* 3.7 34.6 - - + +
514A PHE 6.2 0.2 - - - -
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Residues in contact with ARG 510 (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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505A TYR 3.7 1.0 + - - -
506A GLU* 2.9 36.2 + - - +
507A TYR* 3.0 51.4 + - - +
508A ARG 4.5 2.7 - - - +
509A TYR* 1.3 81.0 - - - +
511A GLY* 1.3 59.4 + - - +
512A LYS* 3.5 6.4 + - - +
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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