Contacts of the helix formed by residues 50 - 63 (chain B) in PDB entry 2JJ7
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 GLY 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ILE* 4.2 21.4 - - - +
45B SER* 4.8 3.0 - - - +
48B PHE* 3.4 3.7 - - - +
49B ASN* 1.3 77.9 - - - +
51B LYS* 1.3 65.1 + - - -
52B GLU* 3.3 4.2 + - - -
53B ASN 3.6 2.0 + - - -
54B LEU* 3.3 20.3 + - - +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.7 13.7 - - + -
25B TYR* 2.5 59.0 + - + +
26B GLU* 3.5 15.4 + - - +
28B THR 2.8 24.4 + - - +
29B SER* 4.8 3.1 - - - +
30B ILE* 4.5 20.4 - - + +
33B ILE* 5.3 0.4 - - + -
50B GLY* 1.3 71.2 - - - -
52B GLU* 1.3 60.4 + - - +
54B LEU* 3.5 10.8 - - + +
55B TYR* 2.8 32.4 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.4 20.7 + - - +
50B GLY 3.3 1.0 - - - -
51B LYS* 1.3 81.1 - - - +
53B ASN* 1.3 58.7 + - - +
55B TYR* 3.3 4.0 - - - +
56B TYR* 3.1 62.0 + - + -
113B ALA* 5.7 1.9 - - - +
114B ARG* 3.2 34.4 + - - +
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR 4.9 1.2 + - - -
48B PHE* 3.0 44.4 + - - +
49B ASN 4.4 4.9 + - - +
50B GLY 3.6 1.9 + - - +
51B LYS 3.3 0.2 - - - -
52B GLU* 1.3 77.9 - - + +
54B LEU* 1.3 60.4 + - - +
56B TYR* 3.2 17.1 + - + +
57B GLU* 2.9 41.6 + - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.9 12.8 - - + -
13B LEU* 3.7 22.9 - - + -
16B ALA* 3.9 11.9 - - + -
20B PHE* 4.3 1.3 - - + -
30B ILE* 4.0 24.5 - - + -
33B ILE* 3.8 35.9 - - + -
48B PHE* 3.5 33.4 - - + +
50B GLY 3.3 9.8 + - - +
51B LYS* 3.5 10.8 - - - +
53B ASN* 1.3 80.3 - - - +
55B TYR* 1.3 56.3 + - - +
57B GLU* 3.2 6.5 + - - +
58B VAL* 2.9 32.9 + - - +
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.7 24.6 - + + -
25B TYR* 3.5 30.8 - + + +
51B LYS 2.8 21.1 + - - +
52B GLU 3.3 4.7 - - - +
54B LEU* 1.3 71.0 - - - +
56B TYR* 1.3 69.7 + + - +
58B VAL* 3.1 13.8 + - + +
59B PHE* 3.1 40.6 + + - -
103B LEU* 4.0 27.4 + - + +
107B GLU* 2.5 41.1 + - - +
114B ARG* 3.7 23.1 - - - -
118B ILE* 4.3 13.7 - - + -
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 3.1 50.2 + - + +
53B ASN* 3.2 21.5 + - - +
55B TYR* 1.3 79.7 - + - +
57B GLU* 1.3 60.6 + - + +
59B PHE* 3.2 5.9 + - - +
60B LYS* 3.0 26.8 + - - +
113B ALA 4.6 2.9 + - - -
114B ARG* 4.0 18.8 - - + -
117B LYS* 3.6 40.8 - - + +
118B ILE* 3.5 27.1 - - + -
121B TYR* 4.8 7.0 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.8 23.0 - - + +
48B PHE* 3.8 23.4 - - + -
53B ASN* 2.9 32.6 + - - +
54B LEU 3.2 5.6 + - - +
56B TYR* 1.3 78.9 - - - +
58B VAL* 1.3 57.0 + - - +
60B LYS* 3.5 34.1 + - - +
61B LYS* 2.8 32.4 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.2 12.1 - - + +
16B ALA* 3.7 28.5 - - + -
17B LYS* 3.8 24.7 - - + +
20B PHE* 4.2 7.4 - - + -
54B LEU 2.9 17.9 + - - +
55B TYR* 3.3 10.8 - - + +
57B GLU* 1.3 74.9 - - - +
59B PHE* 1.3 62.5 + - + +
61B LYS 3.4 0.2 + - - -
62B TYR* 2.9 42.2 + - + +
100B ILE* 4.1 13.9 - - + +
103B LEU* 4.5 15.3 - - + -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 3.1 47.7 + + - +
56B TYR 3.2 7.4 + - - +
58B VAL* 1.3 75.9 - - + +
60B LYS* 1.3 57.2 + - - +
63B GLY* 2.8 31.5 + - - -
100B ILE* 4.3 20.4 - - + -
103B LEU* 3.8 29.6 - - + -
104B ALA* 3.8 20.4 - - + -
118B ILE* 4.0 41.7 - - + -
121B TYR* 3.4 20.1 - - + +
122B PHE* 4.2 27.6 - - + -
123B ILE* 5.2 2.9 - - + -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR 3.0 16.8 + - - +
57B GLU* 3.5 34.8 + - - +
58B VAL 3.3 0.2 - - - -
59B PHE* 1.3 77.9 - - - +
61B LYS* 1.3 61.0 + - - +
63B GLY 4.2 2.6 + - - +
64B LEU 4.7 6.4 - - - +
65B ALA* 5.7 1.6 - - - -
121B TYR* 3.8 45.4 - - + +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 3.2 35.8 + - - +
13B LEU* 3.7 26.7 - - + -
57B GLU 2.8 20.7 + - - +
60B LYS* 1.3 75.6 - - - +
62B TYR* 1.3 101.2 + - + +
63B GLY 3.6 3.3 + - - +
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.5 23.0 - - + -
14B LYS* 3.3 36.2 + - + +
17B LYS* 3.5 49.6 - - + -
58B VAL* 2.9 31.0 + - + +
61B LYS* 1.3 110.7 - - + +
63B GLY* 1.3 56.9 + - - +
93B HIS* 2.7 28.6 + - - -
97B ASN* 3.6 15.7 - - - +
100B ILE* 3.5 17.5 - - + +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL 4.1 0.2 + - - -
59B PHE* 2.8 22.5 + - - -
60B LYS 4.2 1.8 + - - +
61B LYS 3.6 4.8 - - - +
62B TYR* 1.3 82.8 - - - +
64B LEU* 1.3 66.5 + - - -
65B ALA* 3.5 2.3 + - - -
93B HIS* 3.2 18.3 - - - -
100B ILE* 4.3 10.9 - - - +
121B TYR 3.3 8.1 - - - -
122B PHE* 4.8 1.3 - - - -
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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