Contacts of the helix formed by residues 517 - 527 (chain J) in PDB entry 6H25
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 ASN 517 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451J PHE* 2.9 55.6 + - - +
513J ILE* 5.9 1.0 - - - +
514J ARG* 3.5 27.1 + - + +
515J PRO 3.2 3.1 + - - +
516J GLY* 1.3 83.3 - - - +
518J ALA* 1.3 69.4 + - - +
519J LEU* 3.3 12.9 - - + +
520J ASP* 3.2 6.5 + - - +
521J GLN* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 518 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447J ALA* 5.2 4.9 - - + -
448J VAL* 3.7 23.8 - - + +
451J PHE* 3.6 22.0 - - + -
517J ASN* 1.3 77.0 + - - +
519J LEU* 1.3 61.0 + - - +
521J GLN* 3.3 20.4 - - - +
522J GLU* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448J VAL* 3.7 28.6 - - + +
451J PHE* 4.2 18.1 - - + +
452J LEU* 4.1 22.4 - - + -
453J PRO* 6.3 0.2 - - + -
512J PHE* 4.7 6.7 - - + +
513J ILE* 3.7 34.5 - - + -
517J ASN* 3.3 15.1 - - - +
518J ALA* 1.3 78.8 - - - +
520J ASP* 1.3 56.9 + - - +
522J GLU* 3.4 4.7 + - + +
523J SER* 3.0 36.5 + - - +
540J VAL* 5.8 1.3 - - + -
541J PRO* 4.0 26.5 - - + -
544J LEU* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 520 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513J ILE* 3.8 11.4 - - + +
514J ARG 3.7 18.4 - - - +
516J GLY* 3.9 12.3 + - - -
517J ASN* 3.2 13.0 + - - +
519J LEU* 1.3 78.4 - - - +
521J GLN* 1.3 57.2 + - - +
523J SER* 3.7 3.0 - - - +
524J ALA* 2.8 30.0 + - - +
782J TYR* 2.6 34.3 + - - -
789J ARG* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 521 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517J ASN 2.9 12.7 + - - +
518J ALA* 3.1 22.3 + - - +
520J ASP* 1.3 76.7 + - - +
522J GLU* 1.3 58.6 + - + +
524J ALA* 3.3 6.1 + - - +
525J ARG* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 522 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU 5.5 1.2 - - - +
180A ARG* 6.2 0.5 - - - -
444J PHE* 4.3 13.8 - - + -
445J SER* 4.7 13.7 + - - -
448J VAL* 3.8 32.9 - - + +
518J ALA 2.9 7.5 + - - +
519J LEU* 3.4 11.6 + - + +
521J GLN* 1.3 78.1 - - + +
523J SER* 1.3 58.3 + - - +
525J ARG* 3.1 22.5 + - - +
526J ARG* 3.0 65.2 + - - +
539J MET 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513J ILE* 4.3 17.7 - - - +
519J LEU* 3.0 22.6 + - - +
520J ASP* 4.0 2.2 - - - -
522J GLU* 1.3 75.8 - - - +
524J ALA* 1.3 58.3 + - - +
527J GLY* 3.1 20.0 + - - -
539J MET* 3.8 31.9 + - - +
540J VAL* 4.8 4.2 - - - +
782J TYR* 3.3 33.1 - - - +
785J VAL* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520J ASP* 2.8 20.7 + - - +
521J GLN* 3.8 6.1 - - - +
522J GLU 3.2 0.2 - - - -
523J SER* 1.3 77.7 - - - +
525J ARG* 1.3 64.4 + - - +
527J GLY 4.2 2.4 + - - -
782J TYR* 3.7 29.1 - - + +
813J ILE* 6.1 4.9 - - + -
816J ASN* 3.7 17.1 + - - +
817J LEU* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 525 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 3.8 32.3 - - - +
440J PRO* 4.0 26.7 - - + +
442J GLN* 5.4 2.8 + - - -
521J GLN* 2.9 33.1 + - + +
522J GLU* 3.1 22.9 + - - +
524J ALA* 1.3 79.8 - - - +
526J ARG* 1.3 66.3 + - + +
527J GLY* 4.6 0.2 - - - -
816J ASN* 4.7 8.8 - - - +
820J ARG* 3.7 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439J VAL* 6.5 0.2 - - + -
440J PRO* 3.6 41.2 + - + +
441J HIS 5.0 0.4 - - - -
442J GLN 3.0 27.5 + - - -
443J PRO 4.7 0.6 - - - -
444J PHE* 3.2 39.3 - - - +
522J GLU* 3.0 31.9 + - - +
525J ARG* 1.3 76.5 - - + +
527J GLY* 1.3 59.0 + - - +
528J THR* 2.8 20.2 + - - +
537J ILE* 4.2 13.3 - - - +
538J ASP 2.4 32.3 + - - -
539J MET* 3.9 23.5 + - + +
820J ARG* 2.9 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 527 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523J SER 3.1 18.2 + - - -
525J ARG 3.5 1.2 - - - -
526J ARG* 1.3 74.7 - - - +
528J THR* 1.3 58.5 + - - -
539J MET* 3.3 7.0 - - - +
781J ARG* 3.4 2.6 - - - -
782J TYR* 2.8 27.6 + - - +
783J ALA 4.8 0.2 + - - -
817J LEU* 3.4 30.4 - - - +
820J ARG* 4.9 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