Contacts of the helix formed by residues 513 - 523 (chain A) in PDB entry 1N54
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 THR 513 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS 4.5 6.3 - - - +
512A ALA* 1.3 76.7 - - - +
514A ASN* 1.3 70.7 + - - +
515A ASP* 4.2 7.5 + - - +
516A GLU* 3.0 31.9 + - - +
517A ILE* 2.9 25.8 + - - +
568A LYS* 5.1 9.4 - - - +
569A PHE* 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR* 1.3 74.3 - - - +
515A ASP* 1.3 56.9 + - - +
517A ILE* 2.8 6.9 + - - +
518A PHE* 2.7 53.5 + - + -
568A LYS* 3.5 27.6 + - - +
569A PHE* 3.5 7.9 - - - +
571A GLU* 3.3 37.5 - - - +
572A VAL* 3.4 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR* 3.3 7.2 + - - +
514A ASN* 1.3 79.3 + - - +
516A GLU* 1.3 58.2 + - + +
518A PHE* 3.7 20.2 - - - +
519A SER* 3.2 25.5 + - - -
522A LYS* 5.1 0.9 + - - -
571A GLU* 5.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ALA* 5.2 0.7 - - - +
511A LYS 5.0 1.7 - - - +
512A ALA* 3.9 18.6 - - + +
513A THR* 3.0 40.1 + - - +
515A ASP* 1.3 77.5 - - + +
517A ILE* 1.3 60.3 + - - +
519A SER* 4.0 8.2 - - - -
520A ILE* 3.1 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU* 3.7 24.5 - - + -
507A ALA* 3.9 21.8 - - + -
508A PHE* 3.7 19.3 - - + -
512A ALA* 4.0 8.3 - - + -
513A THR 2.9 14.5 + - - +
514A ASN* 2.8 10.6 + - - +
516A GLU* 1.3 78.4 - - - +
518A PHE* 1.3 62.8 + - - +
519A SER 3.2 1.6 - - - -
520A ILE* 3.5 4.4 + - - +
521A LEU* 3.2 34.5 + - + +
547A PHE* 4.0 18.6 - - + -
569A PHE* 3.9 20.6 - - + -
572A VAL* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 2.7 34.0 + - + +
515A ASP* 3.7 18.8 - - - +
517A ILE* 1.3 75.5 - - - +
519A SER* 1.3 56.8 - - - +
521A LEU* 3.1 9.9 + - + +
522A LYS* 2.7 59.1 + - - +
543A LYS* 5.3 9.0 + - - -
571A GLU* 3.8 26.5 - - - -
572A VAL* 3.9 26.5 - - + -
575A THR* 3.3 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASP 3.2 14.9 + - - -
516A GLU* 4.0 10.3 - - - -
518A PHE* 1.3 78.5 - - - +
520A ILE* 1.3 68.6 + - - +
522A LYS* 3.1 29.6 + - - +
523A ASP* 3.8 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A VAL* 3.8 25.7 - - + +
503A CYS* 3.8 33.7 - - + +
504A LEU* 3.8 22.0 - - + +
507A ALA* 4.9 13.2 - - + -
516A GLU 3.1 22.2 - - - +
517A ILE* 3.9 4.0 - - - +
518A PHE 3.3 0.2 - - - -
519A SER* 1.3 78.6 - - - +
521A LEU* 1.3 62.1 + - - +
523A ASP* 3.3 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A VAL* 4.4 2.2 - - + -
504A LEU* 4.0 15.7 - - + -
517A ILE* 3.2 26.5 + - + +
518A PHE* 3.1 9.8 + - + +
520A ILE* 1.3 76.6 - - - +
522A LYS* 1.3 64.7 + - - +
523A ASP 3.0 3.0 + - - -
524A VAL* 3.1 21.4 - - + +
543A LYS* 3.5 59.0 - - + +
546A VAL* 3.8 16.2 - - + -
547A PHE* 4.4 6.5 - - + -
572A VAL* 3.9 27.6 - - + -
576A LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASP 5.1 0.8 + - - -
518A PHE* 2.7 52.7 + - + +
519A SER* 3.1 16.3 + - - +
521A LEU* 1.3 73.1 - - - +
523A ASP* 1.3 57.1 + - - +
524A VAL 3.2 8.9 + - - +
543A LYS* 5.3 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A VAL* 3.7 14.0 - - - +
519A SER 3.8 3.8 + - - +
520A ILE* 3.3 10.1 + - - +
521A LEU 3.0 1.2 - - - -
522A LYS* 1.3 75.4 - - - +
524A VAL* 1.3 65.8 + - - +
525A PRO* 4.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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