Contacts of the helix formed by residues 66 - 78 (chain h) in PDB entry 3J7Y
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 LEU 66 (chain h).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60h TYR* 5.2 0.4 - - - +
62h PRO* 5.8 0.4 - - + -
63h PRO* 3.7 41.8 - - + +
64h GLU 3.9 1.6 - - - -
65h ASP* 1.3 73.2 - - - +
67h GLN* 1.3 64.7 + - + +
68h SER 3.1 1.3 - - - -
69h ARG* 3.6 12.9 - - + +
70h LEU* 2.7 47.9 + - + +
104h LEU* 5.7 1.1 - - + -
108h LEU* 4.4 19.3 - - + -
127h LEU* 3.3 39.3 - - + +
130h TYR* 4.3 21.8 - - + -
131h ASN* 5.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65h ASP 2.6 13.8 + - - +
66h LEU* 1.3 82.3 - - + +
68h SER* 1.3 60.8 + - - +
71h GLU* 3.6 7.6 + - - +
86h TRP* 3.2 43.2 - - - +
87h GLN* 3.2 26.9 + - - +
127h LEU* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65h ASP* 3.9 22.8 + - - +
67h GLN* 1.3 81.4 + - - +
69h ARG* 1.3 66.6 + - - +
70h LEU 3.2 0.2 - - - -
71h GLU* 3.2 10.3 + - - +
72h SER* 2.9 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65h ASP* 5.0 4.3 - - + -
66h LEU* 3.0 21.2 + - + +
68h SER* 1.3 83.8 + - - +
70h LEU* 1.3 57.4 + - - +
72h SER* 3.2 13.9 + - - -
73h TYR* 2.9 46.5 + - + +
76h GLU* 5.7 2.6 + - - -
104h LEU* 6.0 2.2 - - + -
107h ASP* 2.6 32.5 + - + +
108h LEU* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66h LEU* 2.7 26.4 + - + +
67h GLN 4.1 0.2 - - - +
69h ARG* 1.3 74.0 - - - +
71h GLU* 1.3 56.8 + - - +
73h TYR* 3.2 6.0 + - - +
74h VAL* 2.9 42.7 + - + +
86h TRP* 4.0 10.5 - - + -
100h LEU* 4.2 7.6 - - + -
104h LEU* 4.0 33.9 - - + -
123h VAL* 4.1 13.0 - - + +
126h VAL* 4.5 7.4 - - + -
127h LEU* 3.8 46.0 - - + +
130h TYR* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67h GLN* 3.6 10.4 + - - +
68h SER* 3.2 12.6 + - - +
70h LEU* 1.3 79.9 - - - +
72h SER* 1.3 55.9 + - - +
74h VAL* 3.2 4.2 + - - +
75h LYS* 2.9 61.7 + - + +
83h PRO 5.6 0.7 - - - +
86h TRP* 3.1 68.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68h SER* 2.9 17.7 + - - -
69h ARG* 3.3 16.5 - - - -
71h GLU* 1.3 76.4 - - - +
73h TYR* 1.3 56.8 + - - +
75h LYS* 3.2 15.1 + - - +
76h GLU* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69h ARG* 2.9 31.3 + - + +
70h LEU* 3.4 10.5 - - - +
72h SER* 1.3 77.6 - - - +
74h VAL* 1.3 58.1 + - - +
76h GLU* 3.2 23.4 + - + +
77h VAL* 2.9 43.0 + - + +
100h LEU* 4.3 12.6 - - + -
103h HIS* 3.4 42.1 + + + +
104h LEU* 4.1 17.9 - - + -
107h ASP* 2.6 48.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70h LEU* 2.9 35.7 + - + +
71h GLU* 3.4 9.4 - - - +
73h TYR* 1.3 75.1 - - - +
75h LYS* 1.3 55.3 + - + +
77h VAL* 3.2 5.9 + - - +
78h PHE* 2.6 43.0 + - + -
82h LEU 5.0 7.6 - - - +
86h TRP* 4.3 10.5 - - + -
89h ILE* 4.4 23.6 - - + -
100h LEU* 4.2 11.9 - - + -
123h VAL* 4.2 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71h GLU* 2.9 43.7 + - + +
72h SER* 3.4 16.0 + - - +
74h VAL* 1.3 77.6 - - + +
76h GLU* 1.3 63.4 + - + +
78h PHE* 3.3 20.2 - - - -
82h LEU* 3.5 33.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69h ARG* 5.7 2.6 + - - -
72h SER* 2.9 27.8 + - - +
73h TYR* 3.4 25.8 + - + +
75h LYS* 1.3 77.5 - - + +
77h VAL* 1.3 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73h TYR* 2.9 27.8 + - + +
74h VAL* 3.7 5.6 - - - +
75h LYS 4.0 0.2 - - - -
76h GLU* 1.3 81.5 - - + +
78h PHE* 1.3 74.1 + - + +
96h LEU* 3.4 31.2 - - + +
99h ASN* 4.1 20.2 - - + +
100h LEU* 4.6 13.5 - - + +
103h HIS* 4.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74h VAL* 2.6 26.1 + - + +
75h LYS* 3.3 18.4 - - - -
77h VAL* 1.3 93.1 - - + +
82h LEU* 3.3 35.7 - - - +
83h PRO* 5.0 2.2 - - - +
96h LEU* 3.7 40.4 - - + -
99h ASN* 5.8 1.6 - - - -
----------------------------------------------------------
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