Contacts of the helix formed by residues 515 - 523 (chain A) in PDB entry 5XA0
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 ILE 515 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 5.4 2.2 - - + -
446A ALA* 2.8 53.4 - - + +
449A ALA* 3.1 18.8 - - + -
453A LEU* 4.5 2.1 - - + +
480A LEU* 4.7 15.3 - - + -
483A PHE* 6.1 5.4 - - + -
509A LEU* 4.1 0.9 - - + +
510A MET* 3.0 52.5 - - + +
513A GLN 3.0 2.4 + - - -
514A ASN* 1.3 73.8 - - - +
516A LEU* 1.3 59.1 + - - +
518A GLN* 3.5 2.8 + - - +
519A ILE* 2.9 32.1 + - - +
559A VAL* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLN 5.0 0.4 - - - +
510A MET* 2.6 43.9 + - + +
511A ARG* 2.8 64.8 - - + +
515A ILE* 1.3 71.4 - - - +
517A LYS* 1.3 68.3 + - - +
518A GLN 2.9 1.6 - - - -
519A ILE* 2.8 4.3 + - - -
520A PHE* 2.6 68.4 + - + -
563A SER 5.9 0.4 - - - +
564A GLN* 5.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A MET 4.0 0.4 + - - -
511A ARG 4.3 6.1 - - - +
512A GLU 5.3 0.9 - - - +
513A GLN 3.7 13.9 - - - +
514A ASN* 3.5 15.7 - - - +
516A LEU* 1.3 79.2 - - - +
518A GLN* 1.3 66.8 + - - +
520A PHE* 3.1 19.6 + - + +
521A LYS* 3.0 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER* 2.0 23.0 - - - +
453A LEU* 2.6 26.7 - - + +
454A GLY* 1.8 36.4 + - - +
514A ASN* 2.7 40.2 - - - +
515A ILE 3.5 1.5 + - - +
516A LEU 2.9 1.6 + - - -
517A LYS* 1.3 75.3 - - - +
519A ILE* 1.3 52.4 + - - +
521A LYS* 2.5 31.1 + - - +
522A LEU* 2.7 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.6 27.6 - - + -
477A LEU* 6.2 3.1 - - + -
480A LEU* 5.0 9.2 - - + -
510A MET* 4.2 14.1 - - + -
515A ILE 2.9 17.7 + - - +
516A LEU* 2.8 11.9 + - - +
518A GLN* 1.3 69.4 - - - +
520A PHE* 1.3 64.0 + - + +
522A LEU* 2.7 31.8 + - + +
523A LEU* 2.8 29.9 + - + +
556A CYS* 3.5 37.9 - - + -
559A VAL* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 2.6 76.6 + - + -
517A LYS* 3.3 18.8 - - + +
519A ILE* 1.3 81.0 - - + +
521A LYS* 1.3 57.7 + - - +
523A LEU* 2.5 34.6 - - + +
524A GLN* 3.8 1.4 + - - +
560A LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLY* 5.4 0.7 - - - -
457A ALA* 3.9 4.6 - - - +
517A LYS 3.0 8.4 + - - +
518A GLN* 2.5 22.8 + - - +
520A PHE* 1.3 73.3 - - - +
522A LEU* 1.3 71.7 + - + +
524A GLN* 3.4 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 2.5 54.3 - - + +
454A GLY* 3.4 5.8 - - - +
456A ILE* 5.9 0.9 - - + -
457A ALA* 2.7 33.3 - - + +
460A LEU* 5.3 3.5 - - - +
518A GLN* 2.7 44.4 - - - +
519A ILE* 2.7 22.8 + - + +
521A LYS* 1.3 78.5 - - + +
523A LEU* 1.4 54.4 + - - -
524A GLN 2.9 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 2.8 41.9 + - + +
520A PHE* 2.5 51.8 - - + +
522A LEU* 1.4 74.4 - - - +
524A GLN* 1.3 94.5 + - - +
556A CYS* 5.6 1.1 - - - -
----------------------------------------------------------
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