Contacts of the helix formed by residues 508 - 527 (chain B) in PDB entry 4P3N
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 ASP 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507B GLY* 1.3 71.7 - - - -
509B ILE* 1.3 65.6 + - - +
510B GLU* 3.0 35.1 + - - +
511B VAL* 3.6 25.6 + - + +
512B TRP* 3.1 17.9 - - - -
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ARG* 3.6 42.2 - - - +
505B PHE* 4.3 16.4 - - + -
507B GLY 3.7 1.6 + - - -
508B ASP* 1.3 77.0 + - - +
510B GLU* 1.3 63.3 + - - +
512B TRP* 3.2 8.5 + - - +
513B ASP* 2.9 40.9 + - - +
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ASP* 3.0 17.3 + - - +
509B ILE* 1.3 83.1 - - + +
511B VAL* 1.3 61.5 + - + +
513B ASP* 3.1 10.0 + - - +
514B GLN* 2.9 37.9 + - + +
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B MET* 4.0 16.3 - - + +
508B ASP* 3.6 24.8 + - + +
509B ILE 3.3 0.4 - - - -
510B GLU* 1.3 77.5 - - + +
512B TRP* 1.3 62.0 + - - +
513B ASP 3.3 0.2 + - - -
514B GLN* 3.3 11.1 + - - +
515B ALA* 2.9 23.6 + - - +
565B PHE* 3.5 41.7 - - + -
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Residues in contact with TRP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B THR 4.5 0.2 - - - -
501B ARG* 3.4 34.5 - - + +
502B PRO* 4.0 6.5 - - + -
505B PHE* 3.8 16.7 - + + -
506B LEU 2.8 23.1 + - - -
507B GLY* 5.2 0.2 - - - -
508B ASP 3.1 26.2 - - - -
509B ILE* 3.2 13.2 + - - +
511B VAL* 1.3 80.2 - - + +
513B ASP* 1.3 59.3 + - - +
515B ALA* 3.5 5.2 + - - +
516B GLU* 2.9 56.6 + - - +
538B ALA 3.2 23.6 - - - -
539B PHE 3.4 21.8 - - - -
540B TYR 4.1 1.6 - - - -
541B GLY* 3.4 16.4 - - - -
542B PRO* 3.4 25.4 - - + -
565B PHE* 4.1 16.6 - + - -
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Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ARG* 4.9 6.2 + - - -
509B ILE* 2.9 36.4 + - - +
510B GLU* 3.1 10.8 + - - +
512B TRP* 1.3 76.0 - - - +
514B GLN* 1.3 66.1 + - + +
516B GLU* 3.5 11.2 + - - +
517B LYS* 2.9 26.7 + - - +
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Residues in contact with GLN 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B MET* 3.5 35.0 - - + +
470B GLU* 6.2 0.2 - - - +
510B GLU* 2.9 28.5 + - + +
511B VAL* 3.7 6.5 - - - +
513B ASP* 1.3 75.5 - - + +
515B ALA* 1.3 63.7 + - - +
517B LYS* 3.3 5.7 + - - +
518B GLN* 3.0 30.0 + - + +
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Residues in contact with ALA 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B MET* 3.5 13.1 - - + +
472B ILE* 4.3 3.3 - - - +
511B VAL 2.9 16.7 + - - +
512B TRP 3.6 4.5 - - - +
514B GLN* 1.3 77.0 - - - +
516B GLU* 1.3 57.7 + - - +
518B GLN* 3.1 10.0 + - - +
519B LEU* 2.9 31.7 + - - +
542B PRO* 4.4 4.7 - - + -
563B LEU* 3.8 16.8 - - + -
565B PHE* 3.8 23.6 - - + -
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU* 4.7 0.8 - - + +
500B THR* 3.4 27.0 - - + +
501B ARG* 2.8 33.9 + - - +
512B TRP* 2.9 39.4 + - + +
513B ASP* 4.1 11.4 - - - +
515B ALA* 1.3 71.4 - - - +
517B LYS* 1.3 60.0 + - - +
519B LEU* 3.5 10.3 - - + +
520B GLU* 2.9 35.5 + - + +
542B PRO* 3.9 18.6 - - + +
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ASP 2.9 19.2 + - - +
514B GLN* 3.5 7.0 - - - +
516B GLU* 1.3 76.5 - - - +
518B GLN* 1.3 58.6 + - + +
520B GLU* 3.3 7.7 + - - +
521B ASN* 3.0 40.0 + - - +
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Residues in contact with GLN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B MET* 2.7 50.4 + - - +
470B GLU* 3.3 19.4 - - - +
472B ILE* 3.4 12.6 - - + +
473B GLU* 3.4 43.5 + - + +
514B GLN* 3.0 18.1 + - - +
515B ALA 3.5 4.7 - - - +
517B LYS* 1.3 76.1 - - + +
519B LEU* 1.3 58.1 + - - +
521B ASN* 3.3 4.0 + - - +
522B SER* 2.9 33.2 + - - -
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ILE* 4.7 4.0 - - + -
476B ILE* 3.6 34.8 - - + -
498B LEU* 4.1 24.2 - - + -
515B ALA 2.9 17.2 + - - +
516B GLU* 3.5 10.5 - - - +
518B GLN* 1.3 76.9 - - - +
520B GLU* 1.3 56.2 + - - +
522B SER* 3.2 5.7 + - - -
523B LEU* 2.9 34.9 + - - +
542B PRO* 3.8 38.6 - - + -
543B LYS* 4.7 1.1 - - - +
544B ILE* 3.8 20.5 - - + +
561B ILE* 5.9 0.4 - - + +
563B LEU* 4.6 11.9 - - + -
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Residues in contact with GLU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU* 3.9 9.8 - - + +
500B THR* 5.9 1.4 - - + +
516B GLU* 2.9 20.1 + - + +
517B LYS* 3.3 7.2 + - - +
519B LEU* 1.3 75.0 - - - +
521B ASN* 1.3 60.5 + - - +
523B LEU* 3.3 6.8 + - - +
524B ASN* 2.9 44.6 + - - +
530B TRP* 3.8 28.3 - - + -
532B LEU* 4.1 17.9 - - - +
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Residues in contact with ASN 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B GLU* 3.3 35.6 + - - +
517B LYS* 3.0 30.4 + - - +
518B GLN* 3.6 2.5 - - - +
520B GLU* 1.3 78.4 - - - +
522B SER* 1.3 57.1 + - - +
524B ASN* 3.5 7.6 + - - +
525B GLU* 2.9 31.5 + - - +
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Residues in contact with SER 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B GLU* 2.7 35.3 + - - +
476B ILE* 3.7 24.3 - - - +
477B LYS* 4.2 13.4 - - - +
480B LEU* 4.2 3.3 - - - +
518B GLN 2.9 18.6 + - - -
519B LEU 3.6 4.0 - - - -
521B ASN* 1.3 76.5 - - - +
523B LEU* 1.3 57.4 + - - +
525B GLU* 3.3 7.2 + - - +
526B PHE* 2.9 30.8 + - - +
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 4.6 8.7 - - + -
496B LEU* 3.9 33.4 - - + -
498B LEU* 3.6 35.0 - - + +
519B LEU 2.9 19.9 + - - +
520B GLU 3.7 2.7 - - - +
522B SER* 1.3 76.2 - - - +
524B ASN* 1.3 61.6 + - - +
526B PHE* 3.5 16.5 - - - +
527B GLY 3.6 5.2 + - - -
528B GLU 4.1 4.3 - - - +
530B TRP* 3.7 48.2 - - + +
544B ILE* 4.0 28.0 - - + -
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Residues in contact with ASN 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B GLU* 2.9 35.1 + - - +
521B ASN* 3.9 7.7 + - - +
523B LEU* 1.3 74.3 - - - +
525B GLU* 1.3 65.1 + - - +
526B PHE 3.1 2.3 + - - -
527B GLY* 3.2 13.5 + - - -
530B TRP* 3.1 24.3 + - - +
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B GLU* 5.9 1.3 - - - +
477B LYS* 4.3 31.2 + - + +
521B ASN 2.9 19.3 + - - +
522B SER* 3.7 6.7 - - - +
524B ASN* 1.3 76.6 - - - +
526B PHE* 1.3 63.3 + - - +
527B GLY* 4.4 0.9 - - - -
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Residues in contact with PHE 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B LYS* 5.0 5.4 - - + -
480B LEU* 3.6 54.3 - - + -
481B ASP* 4.2 5.6 - - - -
483B LEU* 6.0 0.2 - - + -
484B ARG* 3.2 53.3 + - + -
494B PHE* 4.2 14.1 - + - -
496B LEU* 4.0 28.5 - - + -
522B SER 2.9 17.5 + - - +
523B LEU* 3.5 7.2 - - - +
524B ASN 3.1 0.4 - - - -
525B GLU* 1.3 78.7 - - - +
527B GLY* 1.3 58.7 + - - +
528B GLU* 3.8 9.2 + - + -
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Residues in contact with GLY 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B ARG* 5.3 1.8 - - - -
523B LEU 3.6 2.6 + - - -
524B ASN* 3.2 14.3 + - - -
525B GLU 4.4 0.7 - - - -
526B PHE* 1.3 79.9 - - - +
528B GLU* 1.3 62.1 + - - +
529B LYS 3.8 1.0 + - - -
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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