Contacts of the helix formed by residues 66 - 84 (chain A) in PDB entry 1PJR
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 1.3 70.6 - - - +
67A LYS* 1.4 65.4 + - - +
69A ALA* 3.1 7.2 + - - +
70A ARG* 2.9 24.2 + - - +
91A THR* 3.7 20.0 + - - +
94A SER* 4.6 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.5 9.8 + - - +
66A ASN* 1.4 74.6 - - - +
68A ALA* 1.3 60.0 + - - +
70A ARG* 3.2 12.1 + - - +
71A GLU* 2.8 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.6 26.0 - - + -
65A THR* 3.2 22.8 + - - +
66A ASN 3.2 0.2 - - - -
67A LYS* 1.3 90.2 - - + +
69A ALA* 1.3 61.4 + - - +
71A GLU* 3.4 13.4 - - - +
72A MET* 3.0 29.2 + - + +
223A ASP* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 4.1 13.4 + - - +
65A THR 3.2 9.4 + - - +
66A ASN* 3.1 14.3 + - - +
68A ALA* 1.3 78.4 - - - +
70A ARG* 1.3 57.2 + - - +
72A MET* 3.4 0.9 + - - -
73A ARG* 3.0 27.7 + - - +
89A ILE* 3.4 32.8 - - + +
90A SER* 4.5 13.2 - - - -
91A THR* 4.6 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 2.9 17.2 + - - +
67A LYS* 3.4 10.8 - - - +
69A ALA* 1.3 76.1 - - - +
71A GLU* 1.3 57.5 + - - +
73A ARG* 3.1 10.1 + - + +
74A GLU* 3.0 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.1 12.4 + - + +
67A LYS* 2.8 49.0 + - - +
68A ALA* 3.4 15.5 - - - +
70A ARG* 1.3 68.6 - - - +
72A MET* 1.3 69.4 + - + +
74A GLU* 3.8 16.5 - - - +
75A ARG* 2.8 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 5.3 9.2 - - + -
41A LEU* 4.2 31.6 - - + -
42A THR* 3.7 19.1 - - + -
45A ILE* 4.7 5.2 - - + -
61A ALA* 4.3 24.5 - - - -
62A ILE 5.9 0.9 - - - +
63A THR* 4.1 19.3 - - + +
68A ALA* 3.0 18.1 + - + +
69A ALA 3.6 5.2 - - - +
71A GLU* 1.3 79.1 - - + +
73A ARG* 1.3 55.4 + - - +
75A ARG* 3.4 6.8 + - - +
76A VAL* 3.0 40.6 + - + +
89A ILE* 4.2 13.2 - - + -
223A ASP* 4.4 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 3.0 15.7 + - - +
70A ARG* 3.1 12.5 + - + +
72A MET* 1.3 72.9 - - - +
74A GLU* 1.3 65.5 + - + +
76A VAL* 3.4 2.1 + - - +
77A GLN* 3.0 47.1 + - - +
84A ALA* 2.7 30.8 + - - +
85A GLU* 3.1 17.6 + - - -
87A VAL* 2.6 31.7 + - - +
89A ILE* 3.7 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.0 53.7 + - + +
71A GLU* 3.4 16.8 + - - +
73A ARG* 1.3 74.7 - - + +
75A ARG* 1.3 62.1 + - - +
77A GLN* 3.4 8.0 + - - +
78A SER* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.8 21.9 - - + +
39A ARG* 6.4 0.2 - - - -
42A THR* 3.5 22.4 - - + +
71A GLU* 2.8 65.6 + - - +
72A MET* 3.4 5.4 - - - +
74A GLU* 1.3 78.4 - - - +
76A VAL* 1.3 60.7 + - - +
78A SER* 3.5 13.5 + - - -
79A LEU* 3.7 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 4.1 24.5 - - + +
45A ILE* 4.2 28.5 - - + -
46A ALA* 5.2 2.9 - - + +
49A MET* 4.5 2.9 - - + -
72A MET* 3.0 20.9 + - + +
73A ARG 3.4 3.1 + - - +
75A ARG* 1.3 71.5 - - - +
77A GLN* 1.3 58.2 + - - +
79A LEU* 3.1 11.3 + - - +
80A LEU* 3.0 41.0 + - + +
84A ALA* 3.8 19.7 - - + -
87A VAL* 5.7 0.9 - - + -
89A ILE* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.0 38.5 + - - +
74A GLU* 3.6 7.4 - - - +
76A VAL* 1.3 73.5 - - - +
78A SER* 1.3 61.6 + - - +
81A GLY* 2.8 44.8 + - - +
84A ALA* 3.9 12.0 - - + +
85A GLU* 3.3 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 2.9 16.8 + - - +
75A ARG* 3.7 10.6 - - - -
76A VAL 3.3 0.4 - - - -
77A GLN* 1.3 76.3 - - - +
79A LEU* 1.3 67.2 + - - +
81A GLY 4.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.9 9.8 - - + +
8A LEU* 3.8 21.1 - - + -
42A THR* 4.3 11.2 - - - +
43A HIS* 4.3 24.5 - - + +
46A ALA* 3.8 20.2 - - + -
75A ARG 3.7 17.9 + - - +
76A VAL* 3.1 9.5 + - - +
78A SER* 1.3 87.7 - - - +
80A LEU* 1.3 75.7 + - + +
81A GLY 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.8 18.6 - - + -
8A LEU* 5.0 4.0 - - + -
46A ALA* 3.8 30.3 - - + +
49A MET* 3.5 45.1 - - + -
50A ALA* 5.0 4.9 - - + +
76A VAL* 3.0 16.4 + - + +
79A LEU* 1.3 95.5 - - + +
81A GLY* 1.3 66.2 + - - +
82A GLY 3.7 0.2 + - - -
83A ALA* 3.6 19.9 + - + +
84A ALA 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 2.8 32.7 + - - +
78A SER 4.6 0.8 + - - -
79A LEU 3.7 1.6 + - - -
80A LEU* 1.3 73.0 - - - +
82A GLY* 1.3 59.0 + - - -
83A ALA 2.9 7.3 + - - -
84A ALA* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 5.4 0.2 - - - -
80A LEU 3.7 0.6 + - - -
81A GLY* 1.3 67.3 - - - -
83A ALA* 1.3 61.2 + - - +
84A ALA 3.1 1.2 + - - -
85A GLU* 3.3 36.7 + - - +
86A ASP 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 4.2 12.9 - - - +
56A PRO* 3.5 31.5 - - + +
80A LEU* 3.6 21.2 + - + +
81A GLY 2.9 2.0 + - - -
82A GLY* 1.3 77.4 - - - +
84A ALA* 1.3 60.1 + - - +
85A GLU 3.2 1.1 + - - -
86A ASP* 4.1 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 5.0 1.8 - - - -
73A ARG* 2.7 34.8 + - - +
76A VAL* 3.8 30.3 - - + +
77A GLN* 3.9 24.5 - - + +
80A LEU* 4.8 2.5 - - + +
81A GLY 3.1 13.4 + - - +
82A GLY 3.1 0.4 - - - -
83A ALA* 1.3 76.4 - - - +
85A GLU* 1.3 51.2 + - - +
86A ASP 3.5 0.8 + - - -
87A VAL* 3.7 12.8 + - - +
89A ILE* 5.0 1.1 - - + +
----------------------------------------------------------
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