Contacts of the helix formed by residues 508 - 527 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A GLY* 1.3 72.0 - - - -
509A ILE* 1.3 66.8 + - - +
510A GLU* 2.5 44.0 + - - +
511A VAL* 3.4 22.5 + - + +
512A TRP* 3.0 23.9 + - - -
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Residues in contact with ILE 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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501A ARG* 3.4 45.1 - - - +
505A PHE* 4.3 15.0 - - + -
507A GLY 3.7 2.6 + - - -
508A ASP* 1.3 77.7 + - - +
510A GLU* 1.3 62.5 + - + +
512A TRP* 3.3 8.8 - - + +
513A ASP* 2.9 42.9 + - - +
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Residues in contact with GLU 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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508A ASP* 2.5 21.1 + - - +
509A ILE* 1.3 74.7 - - + +
511A VAL* 1.3 64.7 + - + +
513A ASP* 3.1 10.4 + - - +
514A GLN* 2.9 36.4 + - - +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A MET* 3.6 27.7 - - + +
508A ASP* 3.4 27.3 + - + +
510A GLU* 1.3 77.1 - - + +
512A TRP* 1.3 62.7 - - - +
514A GLN* 3.2 8.8 + - - +
515A ALA* 2.9 22.7 + - - +
565A PHE* 3.6 31.9 - - + -
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Residues in contact with TRP 512 (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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501A ARG* 3.4 44.9 - - + +
502A PRO* 4.0 7.0 - - + -
505A PHE* 3.9 14.3 - + + -
506A LEU 2.7 22.5 + - - -
507A GLY* 4.0 3.3 - - - -
508A ASP 3.0 27.7 + - - -
509A ILE* 3.3 12.5 + - - +
511A VAL* 1.3 79.3 - - - +
513A ASP* 1.3 60.0 + - - +
515A ALA* 3.3 1.4 + - - +
516A GLU* 2.9 47.1 + - - +
538A ALA 3.3 24.0 - - - -
539A PHE 3.4 20.4 - - - -
540A TYR 4.0 1.1 - - - -
541A GLY* 3.3 15.7 - - - -
542A PRO* 3.5 26.0 - - + -
565A PHE* 3.8 21.9 - + - -
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Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ARG* 5.3 4.0 + - - -
509A ILE* 2.9 36.9 + - - +
510A GLU* 3.1 11.1 + - - +
512A TRP* 1.3 76.1 - - - +
514A GLN* 1.3 60.8 + - + +
516A GLU* 4.2 11.2 - - - +
517A LYS* 2.9 31.4 + - - +
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Residues in contact with GLN 514 (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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469A MET* 3.2 30.6 - - + +
470A GLU* 6.1 0.2 - - - +
510A GLU* 2.9 27.3 + - + +
511A VAL* 3.6 8.3 - - - +
513A ASP* 1.3 73.6 - - + +
515A ALA* 1.3 66.3 + - - +
517A LYS* 3.3 5.9 + - - +
518A GLN* 3.0 33.0 + - - +
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Residues in contact with ALA 515 (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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469A MET* 4.0 9.9 - - - -
472A ILE* 4.7 1.9 - - - +
511A VAL 2.9 13.0 + - - +
512A TRP 3.5 7.6 - - - +
514A GLN* 1.3 78.6 - - - +
516A GLU* 1.3 58.1 + - - +
518A GLN* 3.2 6.9 + - - +
519A LEU* 2.9 33.9 + - - +
542A PRO* 4.1 4.7 - - + -
563A LEU* 3.8 19.5 - - + -
565A PHE* 3.6 25.8 - - + -
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Residues in contact with GLU 516 (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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498A LEU* 4.8 1.5 - - + +
500A THR* 3.2 25.6 - - + +
501A ARG* 2.6 40.1 + - - +
512A TRP* 2.9 31.8 + - + +
513A ASP* 4.2 12.6 - - - +
515A ALA* 1.3 70.3 - - - +
517A LYS* 1.3 60.5 + - - +
519A LEU* 3.6 9.3 - - + +
520A GLU* 2.9 42.2 + - + +
542A PRO* 3.9 18.7 - - + +
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Residues in contact with LYS 517 (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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513A ASP 2.9 19.6 + - - +
514A GLN* 3.5 7.2 - - - +
516A GLU* 1.3 75.8 - - - +
518A GLN* 1.3 59.4 + - + +
520A GLU* 3.2 19.9 + - - +
521A ASN* 2.9 54.3 + - - +
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Residues in contact with GLN 518 (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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469A MET* 3.0 48.5 + - - +
470A GLU* 3.4 15.5 - - - +
472A ILE* 3.8 7.5 - - + +
473A GLU* 3.3 51.1 + - + +
514A GLN* 3.0 24.3 + - - +
515A ALA 3.7 2.7 - - - +
517A LYS* 1.3 77.6 - - + +
519A LEU* 1.3 55.4 + - - +
521A ASN* 3.3 5.4 + - - +
522A SER* 2.7 33.7 + - - -
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Residues in contact with LEU 519 (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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472A ILE* 4.5 1.6 - - + -
476A ILE* 3.6 36.6 - - + -
498A LEU* 4.3 22.2 - - + -
515A ALA 2.9 23.7 + - - +
516A GLU* 3.6 9.6 - - - +
518A GLN* 1.3 77.4 - - - +
520A GLU* 1.3 62.8 + - - +
522A SER* 3.0 5.7 + - - -
523A LEU* 2.9 30.5 + - - +
542A PRO* 3.7 39.5 - - + -
543A LYS* 4.7 1.8 - - - +
544A ILE* 4.1 16.8 - - + +
563A LEU* 4.3 15.0 - - + -
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Residues in contact with GLU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 3.8 21.7 - - + +
516A GLU* 2.9 25.8 + - + +
517A LYS* 3.5 21.4 + - + +
519A LEU* 1.3 74.7 - - - +
521A ASN* 1.3 65.1 + - - +
523A LEU* 3.3 7.5 + - - +
524A ASN* 2.9 35.2 + - - +
530A TRP* 4.4 16.2 - - + -
532A LEU* 5.9 5.2 - - - +
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Residues in contact with ASN 521 (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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473A GLU* 3.3 36.8 + - - +
517A LYS* 2.9 42.7 + - - +
518A GLN* 3.5 4.7 - - - +
520A GLU* 1.3 76.9 - - - +
522A SER* 1.3 57.8 + - - +
524A ASN* 3.2 9.8 + - - +
525A GLU* 2.9 28.6 + - - +
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Residues in contact with SER 522 (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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473A GLU* 3.6 26.0 + - - -
476A ILE* 3.6 25.7 - - - +
477A LYS* 4.3 12.2 - - - +
480A LEU* 4.1 3.2 - - - +
518A GLN 2.7 18.8 + - - -
519A LEU* 3.0 8.9 + - - -
521A ASN* 1.3 72.9 - - - +
523A LEU* 1.3 66.2 + - - +
525A GLU* 4.1 5.3 - - - +
526A PHE* 2.9 26.4 + - - +
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Residues in contact with LEU 523 (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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480A LEU* 4.3 14.5 - - + +
496A LEU* 4.4 19.7 - - + +
498A LEU* 3.7 31.9 - - + +
519A LEU 2.9 17.2 + - - +
520A GLU 3.6 4.0 - - - +
522A SER* 1.3 78.5 - - - +
524A ASN* 1.3 59.8 + - - +
526A PHE* 3.5 14.7 + - - +
527A GLY 3.7 4.2 + - - -
528A GLU 4.1 4.2 + - - +
530A TRP* 3.6 57.9 + - + +
544A ILE* 4.2 33.0 - - + -
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Residues in contact with ASN 524 (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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520A GLU* 2.9 27.4 + - - +
521A ASN* 3.6 8.0 + - - +
523A LEU* 1.3 76.1 - - - +
525A GLU* 1.3 62.0 + - - +
526A PHE 3.2 0.4 - - - -
527A GLY* 3.3 13.4 + - - -
530A TRP* 3.0 30.5 + - - +
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Residues in contact with GLU 525 (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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473A GLU* 4.3 13.0 - - - +
477A LYS* 5.5 16.8 - - + +
521A ASN* 2.9 16.0 + - - +
522A SER* 3.7 6.1 - - - +
524A ASN* 1.3 73.9 - - - +
526A PHE* 1.3 63.8 + - - +
527A GLY* 3.2 1.8 + - - -
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Residues in contact with PHE 526 (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 LYS* 5.2 2.0 - - - -
480A LEU* 3.5 54.5 - - + -
481A ASP* 4.2 2.9 - - + -
483A LEU* 6.0 0.2 - - + -
484A ARG* 4.1 43.6 + - + -
494A PHE* 4.1 16.4 - + - -
496A LEU* 3.9 21.1 - - + -
522A SER 2.9 16.6 + - - +
523A LEU* 3.5 8.1 - - - +
524A ASN 3.2 0.2 - - - -
525A GLU* 1.3 79.4 - - - +
527A GLY* 1.3 60.7 + - - +
528A GLU* 3.6 35.4 + - + +
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Residues in contact with GLY 527 (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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523A LEU 3.7 1.2 + - - -
524A ASN 3.3 12.7 + - - -
525A GLU 3.2 3.9 - - - -
526A PHE* 1.3 79.9 - - - +
528A GLU* 1.3 66.9 + - - +
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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