Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 2J0M
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 ASP 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA* 4.9 0.2 - - - +
62A THR* 1.3 96.2 + - + +
64A VAL* 1.3 63.7 + - - +
65A ARG* 4.3 6.1 - - - +
66A GLY* 3.4 17.7 + - - -
67A ILE* 3.3 21.8 + - - +
100A LEU 3.5 11.0 - - - +
101A ASP* 3.4 27.9 - - - +
102A MET 3.3 11.9 - - - +
103A GLY* 3.7 1.6 - - - -
104A VAL* 3.4 17.4 - - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 1.3 76.5 - - - +
65A ARG* 1.3 54.7 + - - +
66A GLY 2.8 6.2 + - - -
67A ILE* 2.7 29.0 + - + +
68A ILE* 3.2 22.1 + - + +
85A LEU* 3.9 30.1 - - + -
98A LEU* 3.9 34.3 - - + +
99A HIS 3.2 27.6 - - - +
100A LEU* 3.2 3.1 + - + +
102A MET 3.2 12.2 + - - +
103A GLY 4.8 1.6 - - - +
104A VAL* 5.8 1.3 - - + -
107A VAL* 4.7 7.2 - - + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 4.3 7.6 - - - +
64A VAL* 1.3 71.5 - - - +
66A GLY* 1.3 61.7 + - - +
68A ILE* 4.3 4.3 - - - +
69A GLN* 2.2 59.8 + - - +
80A VAL* 5.9 0.8 - - - +
100A LEU* 2.6 58.8 + - + +
101A ASP* 5.0 5.2 - - - +
355A THR* 4.3 33.2 + - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP* 5.2 0.2 - - - +
61A ALA* 3.9 22.8 - - - +
63A ASP* 3.4 18.7 + - - -
64A VAL 2.8 2.2 + - - -
65A ARG* 1.3 77.0 - - - +
67A ILE* 1.3 67.1 + - - +
69A GLN* 3.1 13.9 + - - +
70A LYS* 3.2 11.7 + - - +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.9 4.3 - - + -
39A VAL* 4.3 17.0 - - + -
56A ILE* 3.6 31.2 - - + -
60A ASP 5.3 0.4 - - - -
61A ALA* 4.6 8.3 - - - +
63A ASP 3.3 11.3 + - - +
64A VAL* 2.7 19.2 + - + +
66A GLY* 1.3 72.7 - - - +
68A ILE* 1.3 66.5 + - - +
70A LYS* 2.9 15.8 + - - +
71A ILE* 3.2 30.2 + - + +
85A LEU* 4.2 26.2 - - + -
104A VAL* 3.6 24.7 - - + -
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.2 23.5 + - + +
65A ARG* 4.3 3.8 - - - +
67A ILE* 1.3 78.0 - - + +
69A GLN* 1.3 61.1 + - + +
71A ILE* 2.9 7.2 + - - +
72A VAL* 2.8 50.8 + - + +
80A VAL* 4.5 11.4 - - + +
83A TYR* 4.0 29.8 - - + +
84A GLY* 4.3 10.3 - - - -
85A LEU* 4.5 8.1 - - + +
100A LEU* 3.9 28.0 - - + -
124A LEU* 4.2 18.8 - - + -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 2.2 55.5 + - - +
66A GLY* 3.1 5.6 + - - +
68A ILE* 1.3 79.1 - - + +
70A LYS* 1.3 59.8 + - - +
72A VAL* 3.7 7.2 - - + -
73A ASP* 2.9 41.6 + - - +
80A VAL* 4.7 17.5 - - + +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE 5.7 2.7 + - - -
56A ILE* 4.5 21.5 - - + +
57A ARG 6.0 1.2 - - - +
59A GLY 5.2 0.8 + - - -
60A ASP* 4.0 42.4 + - + +
66A GLY 3.2 8.2 + - - +
67A ILE* 2.9 12.5 + - - +
69A GLN* 1.3 79.9 - - - +
71A ILE* 1.3 69.1 + - + +
73A ASP* 3.9 3.0 - - - +
74A CYS* 3.3 27.3 + - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.9 29.8 - - + +
41A HIS* 4.3 6.5 - - - +
43A PHE* 3.6 27.1 - - + -
54A SER* 3.6 36.8 - - - +
56A ILE* 4.5 8.1 - - + -
67A ILE* 3.2 19.0 + - + +
68A ILE* 2.9 8.4 + - - +
70A LYS* 1.3 77.9 - - + +
72A VAL* 1.3 63.4 + - - +
74A CYS* 3.1 9.8 + - - +
75A HIS* 3.0 27.0 - - + +
124A LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.4 4.0 - - + -
68A ILE* 2.8 41.1 + - + +
69A GLN* 3.6 11.2 - - + +
71A ILE* 1.3 73.4 - - - +
73A ASP* 1.3 71.3 + - - +
75A HIS* 3.3 2.8 + - - -
76A LYS 3.2 7.3 + - - -
77A VAL* 3.0 46.4 + - + +
80A VAL* 3.9 22.4 - - + -
83A TYR* 4.1 30.3 - - + -
124A LEU* 4.7 7.9 - - + -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 2.9 34.2 + - - +
70A LYS* 3.9 3.4 - - - +
71A ILE 3.2 1.2 - - - -
72A VAL* 1.3 83.7 - - - +
74A CYS* 1.3 64.1 + - - +
75A HIS 3.1 1.8 - - - -
76A LYS* 3.4 20.6 + - - +
77A VAL 5.1 5.7 - - - +
80A VAL* 5.1 4.0 - - - +
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Residues in contact with CYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 6.1 0.7 - - - -
70A LYS* 3.3 22.1 + - - +
71A ILE* 3.1 14.4 + - + +
73A ASP* 1.3 78.6 - - - +
75A HIS* 1.3 73.4 + - + +
76A LYS* 3.4 4.5 + - - +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A HIS* 4.9 5.7 + + - -
43A PHE* 3.6 61.0 - + + +
44A GLU 5.9 0.7 - - - -
45A ASN* 4.9 12.1 - - - -
54A SER* 5.5 1.4 + - - -
71A ILE* 3.0 30.5 + - - +
72A VAL 3.3 3.5 + - - +
73A ASP 3.1 0.4 - - - -
74A CYS* 1.3 89.1 + - + +
76A LYS* 1.3 70.3 + - - +
77A VAL 3.4 2.0 - - - -
142A PRO* 3.1 24.1 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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