Contacts of the helix formed by residues 60 - 72 (chain A) in PDB entry 4J1O
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 HIS 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PRO* 3.7 9.8 - - - +
54A PRO* 3.9 14.4 - - + +
59A SER* 1.3 81.3 + - - +
61A ALA* 1.3 60.8 + - - +
62A LEU* 3.9 21.9 - - + +
63A GLY* 3.0 36.2 + - - -
64A ALA 2.8 24.8 + - - -
99A TYR* 3.4 8.6 + - - -
409A IOD 3.8 15.0 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.5 41.5 - - + +
33A THR* 4.0 2.6 + - - +
51A PRO* 4.2 5.3 - - - +
60A HIS* 1.3 74.2 - - - +
62A LEU* 1.3 64.5 + - + +
64A ALA* 3.2 8.6 + - - +
65A ARG* 3.1 42.2 + - - +
409A IOD 3.3 16.2 - - + +
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Residues in contact with LEU 62 (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 HIS* 3.4 18.2 - - + +
61A ALA* 1.3 77.5 - - + +
63A GLY* 1.3 58.3 + - - +
65A ARG* 3.5 24.6 + - + +
66A ALA* 3.0 28.2 + - - +
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Residues in contact with GLY 63 (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 HIS* 3.0 25.3 + - - -
62A LEU* 1.3 77.4 - - - +
64A ALA* 1.3 63.5 + - - +
66A ALA* 3.8 6.3 - - - +
67A ALA* 2.9 26.2 + - - +
97A HIS* 5.0 2.5 - - - -
99A TYR* 3.1 18.3 + - - -
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Residues in contact with ALA 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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33A THR* 4.0 10.1 - - + +
49A THR* 3.9 26.7 - - + +
51A PRO* 5.2 1.8 - - + -
60A HIS 2.8 8.6 + - - +
61A ALA* 3.2 11.6 + - - +
63A GLY* 1.3 75.2 - - - +
65A ARG* 1.3 57.7 + - - +
67A ALA* 3.3 2.6 + - - +
68A LEU* 3.0 35.2 + - - +
99A TYR* 3.3 23.3 + - + -
100A ALA* 4.1 5.8 - - + +
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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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8A VAL* 4.2 10.8 - - + +
9A TYR 4.6 0.4 - - - -
10A ALA* 3.5 19.9 - - - +
31A GLN* 2.8 40.0 + - - +
32A THR 3.7 1.6 + - - -
33A THR* 2.9 33.9 + - + +
61A ALA* 3.1 22.1 + - - +
62A LEU* 3.9 26.0 - - + +
64A ALA* 1.3 76.3 - - - +
66A ALA* 1.3 58.0 + - - +
68A LEU* 3.5 6.9 + - - +
69A ALA* 3.0 29.6 + - - +
365A VAL* 4.0 25.3 - - - +
405A IOD 4.2 13.7 - - + -
410A IOD 4.6 2.2 - - - -
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Residues in contact with ALA 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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62A LEU 3.0 17.9 + - - +
63A GLY* 3.8 7.4 - - - +
64A ALA 3.3 0.4 - - - -
65A ARG* 1.3 75.2 - - - +
67A ALA* 1.3 59.8 + - - +
69A ALA* 3.3 2.9 + - - +
70A GLU* 3.0 27.5 + - - +
410A IOD 3.7 23.9 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLY 2.9 18.1 + - - +
66A ALA* 1.3 77.6 - - - +
68A LEU* 1.3 60.2 + - - +
70A GLU* 3.2 6.2 + - - +
71A MET* 3.1 28.7 + - - +
94A LEU* 3.6 22.6 - - + +
97A HIS* 4.0 14.4 - - + -
99A TYR* 5.6 0.4 - - - +
100A ALA* 3.5 24.5 - - + -
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Residues in contact with LEU 68 (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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6A ILE* 6.1 1.1 - - + -
8A VAL* 4.1 18.4 - - + -
33A THR* 3.7 22.0 - - + -
35A VAL* 3.6 30.1 - - + -
49A THR* 5.0 2.0 - - + -
64A ALA* 3.0 24.8 + - + +
65A ARG 3.9 3.6 - - - +
67A ALA* 1.3 76.3 - - - +
69A ALA* 1.3 56.4 + - - +
71A MET* 4.4 8.7 - - + -
72A ALA* 2.8 35.9 + - + +
100A ALA* 3.7 25.8 - - + +
103A ALA* 4.9 4.0 - - + -
104A ILE* 3.8 25.1 - - + -
368A PHE* 5.0 1.8 - - - -
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Residues in contact with ALA 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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8A VAL* 5.4 0.4 - - - +
65A ARG 3.0 18.9 + - - +
66A ALA* 3.6 7.4 - - - +
67A ALA 3.3 0.2 - - - -
68A LEU* 1.3 75.4 - - - +
70A GLU* 1.3 62.0 + - - +
73A PRO* 3.2 21.1 - - - +
366A ALA* 5.7 2.9 - - + -
368A PHE* 3.7 26.1 - - + -
410A IOD 4.6 12.3 - - + -
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Residues in contact with GLU 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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66A ALA 3.0 13.4 + - - +
67A ALA* 3.2 11.2 + - - +
69A ALA* 1.3 79.5 - - - +
71A MET* 1.3 60.4 + - - +
73A PRO* 3.8 6.9 - - - +
74A GLY 5.0 1.4 + - - -
93A LEU* 4.1 23.9 - - - +
94A LEU* 4.5 18.2 - - + -
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Residues in contact with MET 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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67A ALA 3.1 27.2 + - - +
68A LEU* 4.2 11.2 - - + +
70A GLU* 1.3 78.6 - - - +
72A ALA* 1.3 66.4 + - - +
74A GLY 3.0 13.0 + - - -
75A LEU* 3.4 19.1 + - + +
90A MET* 4.0 22.9 - - - +
93A LEU* 3.5 22.9 - - + +
94A LEU* 3.8 31.6 - - + -
100A ALA* 4.2 8.7 - - + -
101A LYS* 3.8 45.5 - - + +
104A ILE* 4.9 1.6 - - + -
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Residues in contact with ALA 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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6A ILE* 3.9 25.4 - - + +
68A LEU* 2.8 22.6 + - + +
71A MET* 1.3 72.9 - - - +
73A PRO* 1.3 68.5 - - + +
75A LEU* 2.9 16.1 + - - +
76A ILE* 3.4 14.7 + - - +
104A ILE* 6.1 1.3 - - + -
368A PHE* 3.4 34.5 - - + -
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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