Contacts of the helix formed by residues 688 - 698 (chain Z) in PDB entry 5L4K
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 ARG 688 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686Z LEU* 3.3 19.3 + - + -
687Z ARG* 1.3 81.6 - - - +
689Z ALA* 1.3 70.8 - - + +
690Z VAL 3.8 0.4 - - - -
691Z PRO* 4.1 10.3 - - - +
692Z LEU* 4.1 15.4 - - - +
720Z GLU* 3.5 27.3 + - - +
721Z VAL* 3.8 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 689 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686Z LEU* 3.8 24.5 - - + +
688Z ARG* 1.3 85.3 - - + +
690Z VAL* 1.3 70.5 + - + +
691Z PRO 3.5 0.3 - - - -
692Z LEU* 3.6 4.3 + - - +
693Z ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 690 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650Z GLN* 4.6 16.4 - - + +
651Z GLY* 5.6 1.8 - - - +
654Z VAL* 3.7 22.2 - - + -
675Z PHE* 3.3 39.9 - - + -
679Z LEU* 4.0 11.0 - - + -
686Z LEU* 4.6 13.8 + - + +
689Z ALA* 1.3 83.5 - - + +
691Z PRO* 1.3 72.0 - - + +
693Z ALA* 2.9 8.8 + - - +
694Z LEU* 2.9 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 691 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679Z LEU* 4.0 19.3 - - + -
686Z LEU 4.9 1.6 - - - +
688Z ARG 4.1 13.0 - - - +
689Z ALA 3.6 2.2 - - - -
690Z VAL* 1.3 96.6 - - + +
692Z LEU* 1.3 57.9 + - - +
694Z LEU 3.5 1.6 + - - -
695Z ALA* 2.9 27.4 + - - +
710Z LEU* 3.7 23.4 - - + +
713Z PHE* 3.9 19.7 - - + -
714Z SER* 3.4 37.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 692 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688Z ARG 4.1 12.1 - - - +
689Z ALA* 3.6 8.0 + - - +
690Z VAL 3.3 0.4 - - - -
691Z PRO* 1.3 81.0 - - + +
693Z ALA* 1.3 58.5 + - - +
695Z ALA* 2.9 23.2 + - + +
696Z LEU* 3.0 15.6 + - + +
714Z SER* 5.1 1.2 + - - +
721Z VAL* 5.4 11.0 - - + -
724Z ASN* 5.4 4.7 - - - +
725Z SER* 3.0 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 693 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654Z VAL* 6.4 0.4 - - + -
689Z ALA 3.2 11.9 + - - +
690Z VAL* 2.9 13.3 + - - +
692Z LEU* 1.3 78.8 - - - +
694Z LEU* 1.3 66.1 + - + +
696Z LEU* 3.8 7.2 + - - +
697Z ILE* 3.2 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 694 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654Z VAL* 4.3 24.7 - - + -
657Z ILE* 4.9 4.5 - - + -
672Z LEU* 3.4 37.9 - - + +
675Z PHE* 3.8 28.0 - - + -
690Z VAL* 2.9 19.7 + - + +
693Z ALA* 1.3 82.0 - - + +
695Z ALA* 1.3 59.8 + - - +
696Z LEU 3.4 0.4 - - - -
697Z ILE* 3.9 19.4 - - + +
698Z SER* 3.3 26.5 + - - +
706Z ILE* 4.5 0.6 - - + +
710Z LEU* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 695 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691Z PRO 2.9 16.8 + - - +
692Z LEU* 2.9 16.2 + - + +
694Z LEU* 1.3 77.6 - - - +
696Z LEU* 1.3 59.3 + - - +
699Z VAL* 3.1 31.4 + - - +
707Z LEU* 3.6 15.5 - - + +
710Z LEU* 3.8 9.9 - - + -
725Z SER* 5.2 7.9 - - - +
729Z MET* 5.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 696 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692Z LEU* 3.0 13.6 + - + +
693Z ALA* 4.1 7.0 - - - +
695Z ALA* 1.3 76.1 - - - +
697Z ILE* 1.3 66.4 + - + +
699Z VAL* 3.6 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 697 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672Z LEU* 4.8 12.6 - - + -
693Z ALA* 3.2 20.4 + - + +
694Z LEU* 3.8 28.9 + - + +
695Z ALA 3.4 0.2 - - - -
696Z LEU* 1.3 81.3 - - + +
698Z SER* 1.3 62.7 + - - +
699Z VAL* 3.3 2.6 + - - +
700Z SER 4.2 1.2 + - - -
701Z ASN* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 698 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672Z LEU* 4.2 13.3 - - - +
694Z LEU* 3.3 11.9 + - - +
697Z ILE* 1.3 80.6 - - - +
699Z VAL* 1.3 63.1 + - - +
700Z SER 3.1 2.4 + - - -
701Z ASN* 3.8 20.6 + - - +
703Z ARG 4.9 0.3 - - - +
704Z LEU* 4.5 0.5 - - - +
706Z ILE* 3.4 50.0 - - - +
707Z LEU* 3.3 22.1 - - - +
----------------------------------------------------------
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