Contacts of the helix formed by residues 55 - 66 (chain B) in PDB entry 2J7Z
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU 4.5 0.2 - - - +
16B SER 3.3 30.1 - - - +
18B VAL* 4.2 9.9 - - + +
51B ILE* 4.4 9.2 - - + -
52B ASP* 3.1 37.6 + - + +
53B PRO 3.3 2.0 - - - +
54B LYS* 1.3 77.0 - - - +
56B LYS* 1.3 67.3 + - - +
57B TRP* 3.3 37.2 - - + +
58B ILE* 3.1 27.9 + - + +
59B GLN* 4.0 2.1 + - - +
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Residues in contact with LYS 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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54B LYS 3.1 11.1 + - - +
55B LEU* 1.3 73.8 - - - +
57B TRP* 1.3 63.9 + - - +
58B ILE 3.1 0.7 + - - -
59B GLN* 3.2 23.2 + - - +
60B GLU* 3.7 4.9 + - - +
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Residues in contact with TRP 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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18B VAL* 2.8 31.8 + - + -
19B ALA* 5.2 0.7 - - - -
20B ARG* 3.7 51.2 + - + +
23B VAL* 3.7 25.8 - - + -
26B LEU* 4.1 16.8 - - + -
51B ILE* 4.1 26.0 - - + -
55B LEU* 3.7 26.8 - - + +
56B LYS* 1.3 78.1 - - - +
58B ILE* 1.3 68.4 + - + +
60B GLU* 3.3 9.5 + - + +
61B TYR* 2.9 39.0 + + + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.7 25.4 - - + -
26B LEU* 4.3 8.7 - - + -
38B ILE* 4.2 9.0 - - + -
51B ILE* 3.4 31.4 - - + -
52B ASP 3.3 26.7 - - - +
53B PRO* 4.2 10.1 - - + +
55B LEU* 3.1 19.9 + - + +
57B TRP* 1.3 92.3 - - + +
59B GLN* 1.3 66.7 + - - +
61B TYR* 3.2 3.2 + - - +
62B LEU* 2.9 36.2 + - + +
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Residues in contact with GLN 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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66A LEU* 4.4 22.0 - - + +
55B LEU 4.0 1.8 + - - +
56B LYS* 3.2 15.6 + - - +
58B ILE* 1.3 79.1 - - - +
60B GLU* 1.3 63.6 + - - +
62B LEU* 3.5 2.0 + - - +
63B GLU* 3.0 51.1 + - + +
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Residues in contact with GLU 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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20B ARG* 3.8 16.8 - - - +
56B LYS 3.7 4.3 + - - +
57B TRP* 3.3 13.8 + - - +
58B ILE 3.2 0.4 - - - -
59B GLN* 1.3 77.9 - - - +
61B TYR* 1.3 64.0 + - - +
63B GLU* 3.3 16.1 + - - +
64B LYS* 3.0 38.4 + - + +
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Residues in contact with TYR 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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28A ILE* 2.8 42.0 + - + -
29A LEU 4.0 3.1 - - - -
30A ASN* 3.0 49.0 + - - +
37A GLN* 4.7 5.8 - - - +
20B ARG* 3.3 41.1 + - + +
23B VAL* 4.5 3.2 - - + +
25B HIS* 3.6 6.4 - - - -
26B LEU* 3.6 31.0 - - + -
57B TRP* 2.9 23.1 + + + +
58B ILE* 3.3 12.1 - - - +
60B GLU* 1.3 79.2 - - - +
62B LEU* 1.3 68.1 + - + +
64B LYS* 3.5 4.2 + - - +
65B ALA* 3.2 19.9 + - - +
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Residues in contact with LEU 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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28A ILE* 3.8 29.6 - - + -
62A LEU* 4.3 34.7 - - + +
66A LEU* 4.0 24.0 - - + -
26B LEU* 4.7 3.4 - - + -
28B ILE* 4.5 13.9 - - + -
38B ILE* 5.4 0.7 - - + -
58B ILE* 2.9 34.8 + - + +
59B GLN* 4.0 3.4 - - - +
61B TYR* 1.3 87.1 - - + +
63B GLU* 1.3 66.0 + - + +
65B ALA* 3.1 7.0 + - + +
66B LEU* 3.1 28.3 + - + +
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Residues in contact with GLU 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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59B GLN* 3.0 52.9 + - + +
60B GLU* 3.3 16.4 + - - +
62B LEU* 1.3 74.7 - - + +
64B LYS* 1.3 63.3 + - + +
66B LEU* 3.1 18.2 + - + +
68B LYS* 3.2 40.5 + - + +
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Residues in contact with LYS 64 (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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32A PRO* 4.1 22.2 - - - +
37A GLN* 3.8 13.4 + - - +
20B ARG* 3.7 33.0 - - - +
60B GLU* 3.0 33.3 + - - +
61B TYR 3.8 4.9 - - - +
63B GLU* 1.3 77.4 - - + +
65B ALA* 1.3 58.2 + - - +
67B ASN* 3.0 23.9 + - - +
68B LYS* 5.1 1.1 - - - +
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Residues in contact with ALA 65 (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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28A ILE* 3.6 31.6 - - + -
35A ALA 5.2 0.9 - - - +
37A GLN* 3.6 26.7 + - + +
38A ILE* 4.0 20.5 - - + +
53A PRO* 4.1 5.9 - - - +
62A LEU* 6.1 1.3 - - + -
61B TYR 3.2 8.5 + - - +
62B LEU* 3.1 12.2 + - + +
64B LYS* 1.3 79.0 - - - +
66B LEU* 1.3 61.9 + - + +
67B ASN* 3.2 9.2 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.0 9.0 - - + -
53A PRO* 3.9 24.1 - - - +
54A LYS* 6.1 0.5 - - - +
58A ILE* 3.7 29.6 - - + -
59A GLN* 4.2 29.8 - - + +
62A LEU* 3.9 16.6 - - + -
63A GLU* 6.4 0.4 - - + -
62B LEU* 3.1 19.4 + - + +
63B GLU* 3.6 11.7 - - + +
64B LYS 3.1 0.4 - - - -
65B ALA* 1.3 75.8 - - - +
67B ASN* 1.3 72.7 + - - +
68B LYS* 3.0 22.8 + - + +
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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