Contacts of the helix formed by residues 67 - 77 (chain V) in PDB entry 5JPQ
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 ALA 67 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354T PHE* 4.0 22.4 - - + -
9V TYR* 4.2 21.1 - - + +
63V GLU 3.8 4.1 + - - +
64V GLU* 3.1 26.8 + - - +
66V VAL* 1.3 77.1 - - - +
68V HIS* 1.3 60.1 + - - +
69V LEU 3.3 0.6 + - - -
70V PRO* 4.1 10.8 - - - +
71V LEU* 4.5 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T ALA* 4.1 22.9 - - + +
289T LYS* 4.4 15.2 - - + +
350T ARG* 5.9 3.8 - - + -
64V GLU 4.5 2.1 + - - +
65V ILE 5.8 2.0 - - - +
66V VAL 3.1 1.4 + - - -
67V ALA* 1.3 78.7 - - - +
69V LEU* 1.3 57.9 + - - +
70V PRO 3.5 0.2 - - - -
71V LEU* 3.3 10.8 + - + +
72V LEU* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V VAL* 6.2 4.0 - - + -
56V ILE* 5.8 7.4 - - + -
66V VAL* 3.1 19.5 + - + +
68V HIS* 1.3 74.8 - - - +
70V PRO* 1.3 68.3 - - - +
72V LEU* 3.8 6.5 - - - +
73V CYS* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V TYR* 4.7 13.9 - - + +
11V LYS* 5.6 8.7 - - + -
66V VAL 4.4 1.4 - - - -
67V ALA 4.1 8.8 - - - +
68V HIS 3.5 0.6 - - - -
69V LEU* 1.3 79.2 - - - +
71V LEU* 1.3 62.5 + - - +
73V CYS* 3.9 3.9 - - + +
74V ASP* 3.2 22.5 + - - +
80V TYR* 5.9 4.5 - - + -
112X ARG* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67V ALA 4.5 2.8 + - - +
68V HIS* 3.3 14.4 + - - +
69V LEU 3.2 0.6 - - - -
70V PRO* 1.3 79.3 - - - +
72V LEU* 1.3 61.8 + - - +
74V ASP* 3.6 5.0 + - - +
75V GLU* 3.4 19.9 + - - +
112X ARG* 3.8 39.6 - - + +
113X VAL* 4.5 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289T LYS* 5.8 7.9 - - + +
46V VAL* 5.1 13.6 - - + +
68V HIS* 3.0 17.7 + - + +
69V LEU* 3.1 7.4 + - - +
71V LEU* 1.3 77.0 - - - +
73V CYS* 1.3 63.0 + - - +
75V GLU* 3.4 8.5 + - - +
76V LYS* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 73 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V VAL* 5.2 7.7 - - + +
54V VAL* 5.5 5.4 - - + -
69V LEU* 2.9 18.3 + - + +
70V PRO* 3.9 5.2 - - + +
72V LEU* 1.3 77.3 - - - +
74V ASP* 1.3 51.5 + - - +
76V LYS* 3.5 2.1 + - - +
77V LYS* 2.7 28.9 + - - -
78V ILE* 2.8 39.7 + - + +
80V TYR* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70V PRO 3.2 15.5 + - - +
71V LEU* 3.9 6.3 - - - +
72V LEU 3.3 0.4 - - - -
73V CYS* 1.3 76.5 - - - +
75V GLU* 1.3 63.8 + - - +
77V LYS* 3.4 14.0 + - - +
86X ALA* 4.9 4.2 - - - +
113X VAL* 5.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71V LEU 3.4 9.7 + - - +
72V LEU* 3.4 12.2 + - - +
74V ASP* 1.3 79.4 - - - +
76V LYS* 1.3 60.4 + - - +
77V LYS* 3.6 1.6 + - - +
86X ALA* 4.0 17.9 - - + +
87X SER* 4.0 30.5 - - - +
113X VAL* 5.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V VAL* 4.0 22.7 - - - +
49V GLY* 5.4 5.8 - - - -
72V LEU 3.2 13.1 + - - +
73V CYS* 4.3 4.0 - - - +
75V GLU* 1.3 77.0 - - + +
77V LYS* 1.3 69.7 + - - +
78V ILE* 3.3 8.9 + - + +
58X ARG 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73V CYS 2.7 9.8 + - - -
74V ASP* 3.4 10.3 + - - +
75V GLU 3.3 4.5 - - - +
76V LYS* 1.3 80.6 - - - +
78V ILE* 1.3 56.5 + - - +
79V PRO 4.1 1.4 - - - -
155X ALA* 5.5 10.5 - - + -
----------------------------------------------------------
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