Contacts of the helix formed by residues 669 - 679 (chain J) in PDB entry 4XLN
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 669 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662J GLU* 3.6 19.8 - - - +
667J ALA* 3.5 3.0 - - - +
668J PRO* 1.3 86.3 - - - +
670J VAL* 1.3 70.1 + - + +
671J LYS* 3.9 22.5 - - - +
672J ALA* 3.4 17.3 + - - +
673J ALA* 3.4 17.5 + - - +
364L LEU* 4.7 8.8 - - + +
368L GLU* 4.2 17.8 + - - +
432L LYS* 4.2 25.5 + - - +
435L ASP* 5.8 1.4 - - - +
436L PHE* 4.3 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 670 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067I TYR* 5.5 2.7 - - + +
1071I ILE* 3.7 47.6 - - + +
658J LEU* 3.0 33.3 - - + +
662J GLU* 3.7 17.3 - - + +
669J ASN* 1.3 76.3 - - + +
671J LYS* 1.3 65.8 + - + +
673J ALA* 3.1 4.9 + - - -
674J ARG* 2.9 20.6 + - + -
364L LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 671 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669J ASN* 3.5 10.9 - - - +
670J VAL* 1.3 75.6 - - + +
672J ALA* 1.3 64.6 + - - +
674J ARG* 3.2 27.6 + - - +
675J ARG* 2.9 30.0 + - - +
357L VAL 5.2 0.6 + - - -
361L ALA* 3.5 31.2 - - - +
364L LEU* 4.0 23.1 - - + -
435L ASP* 3.9 12.5 - - + +
436L PHE* 3.5 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 672 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667J ALA* 3.4 22.4 - - + -
668J PRO* 3.5 14.4 - - + -
669J ASN* 3.4 21.6 + - - +
670J VAL 3.1 0.2 + - - -
671J LYS* 1.3 79.9 - - - +
673J ALA* 1.3 57.1 + - - +
675J ARG* 3.3 3.0 + - - +
676J MET* 2.9 32.2 + - + +
435L ASP* 4.1 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 673 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658J LEU* 3.8 14.4 - - + +
661J MET* 3.6 39.7 - - + -
667J ALA* 3.5 10.2 - - + +
669J ASN 3.4 7.0 + - - +
670J VAL 3.1 8.3 + - - +
672J ALA* 1.3 78.7 - - - +
674J ARG* 1.3 62.4 + - - +
676J MET* 3.3 9.2 + - - +
677J LEU* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 674 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067I TYR* 3.7 20.1 + - - -
654J LYS* 4.5 17.8 - - - +
658J LEU* 3.3 20.0 - - + +
670J VAL* 2.9 14.3 + - - +
671J LYS* 3.3 34.5 - - - +
672J ALA 3.2 0.2 - - - -
673J ALA* 1.3 75.8 - - - +
675J ARG* 1.3 64.2 + - - +
677J LEU* 2.9 6.5 + - - +
678J GLU* 2.7 65.9 + - + +
357L VAL* 3.5 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 675 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671J LYS* 2.9 21.8 + - - +
672J ALA* 3.9 2.9 - - - +
674J ARG* 1.3 75.5 - - - +
676J MET* 1.3 61.9 + - - +
677J LEU 3.4 0.3 + - - -
678J GLU* 4.4 15.6 + - - -
679J ARG* 3.2 75.8 + - - +
435L ASP* 3.6 28.9 + - - +
436L PHE* 4.1 8.7 - - - +
437L LEU* 3.3 28.5 - - - +
438L GLU* 3.9 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 676 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661J MET* 4.7 5.6 - - + -
666J PHE* 4.5 18.6 - - + -
667J ALA* 3.9 34.1 - - + +
672J ALA* 2.9 14.8 + - + +
673J ALA* 3.3 12.6 - - - +
674J ARG 3.1 0.2 - - - -
675J ARG* 1.3 76.6 - - - +
677J LEU* 1.3 62.1 + - - +
679J ARG 3.4 12.2 - - - +
680J GLN 4.1 0.7 - - - +
682J ASP* 3.9 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 677 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650J LEU* 4.4 22.0 - - + +
654J LYS* 4.6 13.2 - - + -
657J LEU* 3.7 21.8 - - + -
658J LEU* 3.7 24.0 - - + -
661J MET* 3.6 36.6 - - + -
673J ALA 2.9 12.9 + - - +
674J ARG* 3.6 5.6 - - - +
676J MET* 1.3 77.5 - - - +
678J GLU* 1.3 69.0 + - + +
679J ARG 3.9 2.1 - - - +
680J GLN 4.9 1.9 - - - +
681J ARG* 4.9 7.4 - - - +
682J ASP* 6.1 1.3 - - - +
683J ILE* 5.6 3.4 - - + -
687J VAL* 4.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 678 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654J LYS* 4.5 17.1 + - - +
674J ARG* 2.7 64.9 + - + +
675J ARG* 3.5 17.9 + - - +
677J LEU* 1.3 80.9 - - - +
679J ARG* 1.3 66.6 + - + +
680J GLN 3.9 1.0 + - - -
681J ARG* 5.0 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 679 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730I SER* 5.8 5.5 + - - -
752I GLY* 6.5 1.6 - - - -
791I ARG* 5.2 14.8 - - - +
675J ARG* 3.2 53.8 + - - +
676J MET* 3.4 13.2 - - - +
677J LEU 3.9 0.3 - - - +
678J GLU* 1.3 81.3 + - + +
680J GLN* 1.3 78.0 + - + +
437L LEU* 5.3 2.8 - - - +
438L GLU 3.1 26.3 + - - -
----------------------------------------------------------
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