Contacts of the helix formed by residues 72 - 81 (chain 1) in PDB entry 5KZ5
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 72 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 ASP* 3.2 21.9 + - - +
711 PRO* 1.3 76.3 - - - +
731 VAL* 1.4 64.8 + - - +
741 LEU 3.4 0.2 - - - -
751 ASP* 3.8 9.6 - - + +
761 ALA* 2.9 30.3 + - + +
77G ASN* 3.9 5.1 - - - +
78G LEU 4.2 1.6 + - - -
79G ARG* 3.6 30.4 + - - +
80G LYS 3.4 25.1 + - - +
81G SER 3.2 28.4 + - - -
82G GLY* 3.9 10.1 - - - -
83G THR* 4.0 16.6 + - - +
208G LYS* 5.5 0.4 - - - +
45I ASP* 4.1 10.0 + - - -
48I ALA* 4.0 2.5 - - + -
49I THR 3.8 21.5 - - - +
54I ARG* 3.5 25.2 - - - +
84g LYS* 4.3 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 ASP 3.7 13.0 - - - +
711 PRO 3.2 0.8 + - - -
721 ARG* 1.4 74.1 - - - +
741 LEU* 1.4 61.6 + - - +
771 MET* 3.3 24.0 + - - +
2621 PRO* 4.7 8.3 - - + -
3031 GLY* 3.8 19.5 - - - +
3061 ALA* 3.7 20.9 - - + -
3071 ALA 4.6 0.7 - - - +
210G ALA* 4.2 16.4 - - + +
47I ASP 3.4 24.9 - - - +
48I ALA* 3.7 8.0 - - + +
49I THR* 3.5 27.9 + - - +
453P LYS* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO 3.7 1.6 + - - -
731 VAL* 1.4 76.5 - - - +
751 ASP* 1.3 65.4 + - - +
771 MET* 3.5 17.2 + - + +
781 LEU* 3.1 29.8 + - + +
202G SER* 3.9 26.9 - - - -
203G LEU 3.8 20.0 - - - +
207G GLY* 3.8 13.0 - - - -
208G LYS* 3.6 20.2 - - - +
209G ASP* 3.5 26.0 - - - +
210G ALA* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO 3.8 10.6 + - - +
721 ARG* 3.6 13.5 - - + +
731 VAL 3.3 0.2 - - - -
741 LEU* 1.3 79.2 - - - +
761 ALA* 1.3 56.8 + - - +
781 LEU* 3.9 4.3 - - - +
791 PRO* 3.1 25.8 - - - +
83G THR 3.3 13.7 - - - +
84G LEU 3.3 5.9 - - - +
85G GLY 3.1 26.6 + - - -
86G HIS* 3.9 12.1 - - - -
87G PRO 3.4 19.1 - - - +
208G LYS* 3.8 30.0 + - - +
54I ARG* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721 ARG* 2.9 22.0 + - + +
731 VAL 4.0 0.4 - - - +
751 ASP* 1.3 73.8 + - - +
771 MET* 1.4 63.9 + - - +
781 LEU 3.6 0.2 + - - -
791 PRO* 3.6 16.4 - - - +
84G LEU 6.1 0.2 - - - -
49I THR* 3.8 31.0 - - + -
51I THR* 6.4 0.2 - - + -
54I ARG* 4.4 22.9 - - - +
453P LYS* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 VAL 3.3 16.8 + - - +
741 LEU* 3.7 18.2 - - + +
751 ASP 3.4 0.2 - - - -
761 ALA* 1.4 78.2 - - - +
781 LEU* 1.4 62.0 + - - +
791 PRO 3.4 6.2 - - - +
801 TYR* 3.2 53.3 - - + +
851 TYR* 6.2 2.0 - - + -
3021 VAL* 4.0 32.8 - - + -
3031 GLY* 5.5 4.9 - - - -
120D PHE* 4.5 18.6 - - + -
453P LYS* 4.6 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 LEU* 3.1 22.9 + - + +
751 ASP* 3.9 4.0 - - - +
771 MET* 1.4 72.5 - - - +
791 PRO* 1.3 72.5 - - + +
801 TYR* 3.2 10.3 + - - +
811 LEU* 4.0 10.3 - - + +
851 TYR* 4.1 16.2 - - + +
86G HIS* 5.6 0.7 - - - +
87G PRO* 3.9 34.5 - - + +
91G ASP* 4.6 13.5 - - + +
203G LEU 5.6 1.8 - - - +
204G ALA 3.4 26.5 - - - +
205G TYR* 4.7 13.9 - - + -
206G SER 6.1 1.1 - - - +
207G GLY 5.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751 ASP 3.1 22.2 - - - +
761 ALA* 3.6 12.7 - - - +
771 MET 3.4 4.5 - - - +
781 LEU* 1.3 86.8 - - + +
801 TYR* 1.3 72.9 + - - +
811 LEU* 4.7 2.9 - - + -
84G LEU 5.5 2.7 - - - +
88G GLY* 3.9 26.0 - - - -
89G SER* 4.0 6.5 - - - +
90G LEU* 4.1 29.4 - - + +
91G ASP* 5.3 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 MET* 3.2 51.9 - - + +
781 LEU* 3.2 8.4 + - - +
791 PRO* 1.3 83.2 - - - +
811 LEU* 1.4 70.1 + - - +
821 ILE* 3.1 14.1 + - - +
841 TYR* 3.6 35.4 - - + -
851 TYR* 3.7 45.1 - + + +
861 GLY 5.7 0.2 - - - -
981 GLU* 5.9 3.1 - - + -
120D PHE* 6.1 1.9 - + - -
90G LEU* 3.6 23.5 - - - +
93G THR* 4.8 0.2 + - - -
450P LYS* 6.5 1.3 - - - -
453P LYS* 5.6 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 LEU* 4.0 13.7 - - + +
791 PRO* 4.7 0.4 - - + -
801 TYR* 1.4 85.3 - - - +
821 ILE* 1.4 64.9 + - - +
831 ASN* 3.5 2.6 + - - -
851 TYR* 3.6 17.1 - - + +
138D GLY 4.1 6.2 - - - +
139D ASP* 3.8 35.4 - - + +
140D LEU* 4.1 17.7 - - - +
90G LEU 3.4 25.1 - - - +
91G ASP* 3.9 24.9 - - - +
93G THR* 4.3 5.8 - - - -
94G THR* 3.6 38.8 - - + +
----------------------------------------------------------
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