Contacts of the helix formed by residues 45 - 58 (chain A) in PDB entry 2J7J
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.8 4.8 - - - -
43A PHE* 3.4 5.5 - - - +
44A SER* 1.3 96.1 + - - +
46A PRO* 1.3 76.9 - - + +
47A SER* 3.9 15.7 - - - +
48A ARG* 3.2 47.4 + - + +
49A LEU* 3.3 10.0 + - - +
1089A SO4 4.4 7.4 - - - +
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Residues in contact with PRO 46 (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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32A TYR* 3.6 43.0 - - + +
44A SER 4.5 0.2 - - - +
45A LEU* 1.3 93.0 - - + +
47A SER* 1.3 56.1 + - - +
49A LEU* 3.2 6.8 + - + +
50A LYS* 3.0 29.0 + - - +
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Residues in contact with SER 47 (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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45A LEU* 3.9 14.0 - - - +
46A PRO* 1.3 79.4 - - - +
48A ARG* 1.3 63.7 + - - +
50A LYS* 3.4 8.0 + - - +
51A ARG* 3.1 29.3 + - - +
1089A SO4 4.3 8.1 + - - -
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Residues in contact with ARG 48 (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* 3.6 30.8 - - + -
44A SER* 3.4 22.8 + - - +
45A LEU* 3.2 33.8 + - + +
47A SER* 1.3 74.0 + - - +
49A LEU* 1.3 64.8 + - - +
51A ARG* 3.6 26.6 + - - +
52A HIS* 3.1 22.9 + - - +
1089A SO4 3.1 41.4 + - - +
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Residues in contact with LEU 49 (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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32A TYR* 3.9 35.7 - - + -
33A GLU 3.7 15.7 - - - +
34A CYS* 3.7 31.6 - - + +
35A PRO* 5.1 0.7 - - + -
43A PHE* 3.7 19.6 - - + -
45A LEU 3.3 3.0 + - - +
46A PRO* 3.2 9.0 + - + +
48A ARG* 1.3 78.0 - - - +
50A LYS* 1.3 59.6 + - - +
52A HIS* 3.1 3.6 + - + +
53A GLU* 2.9 48.1 + - + +
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Residues in contact with LYS 50 (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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46A PRO 3.0 15.2 + - - +
47A SER* 3.7 8.3 - - - +
48A ARG 3.3 0.2 - - - -
49A LEU* 1.3 77.4 - - - +
51A ARG* 1.3 62.5 + - - +
53A GLU* 3.2 10.5 + - + +
54A LYS* 3.0 50.5 + - + +
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Residues in contact with ARG 51 (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* 6.1 1.0 - - - -
47A SER 3.1 17.0 + - - +
48A ARG* 3.7 27.4 + - - +
50A LYS* 1.3 75.7 - - - +
52A HIS* 1.3 63.2 + - - +
54A LYS* 3.2 14.3 + - + +
55A VAL* 3.1 28.2 + - + +
1089A SO4 2.9 42.8 + - - -
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Residues in contact with HIS 52 (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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34A CYS* 3.7 14.1 - - + -
39A CYS* 4.2 0.9 - - - -
41A LYS* 3.5 27.6 - - + +
43A PHE* 3.4 37.7 - + + -
48A ARG 3.1 11.2 + - - +
49A LEU* 3.1 6.9 + - + +
51A ARG* 1.3 78.4 - - - +
53A GLU* 1.3 61.0 + - - +
55A VAL* 3.2 25.7 + - + +
56A HIS* 3.2 22.4 + + - -
1087A ZN 2.2 36.3 - - - -
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Residues in contact with GLU 53 (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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34A CYS* 4.9 2.7 - - - -
35A PRO* 3.4 41.2 - - + +
36A HIS* 4.3 13.5 - - + +
49A LEU* 2.9 35.0 + - + +
50A LYS* 3.2 11.3 + - + +
52A HIS* 1.3 75.1 - - - +
54A LYS* 1.3 62.5 + - + +
56A HIS* 3.2 23.1 + - - +
57A ALA* 3.3 7.4 + - - +
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Residues in contact with LYS 54 (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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50A LYS* 3.0 45.7 + - + +
51A ARG* 3.5 14.3 - - - +
52A HIS 3.2 0.2 - - - -
53A GLU* 1.3 73.5 - - + +
55A VAL* 1.3 64.8 + - + +
57A ALA* 3.1 18.5 + - - +
58A GLY* 3.3 9.2 + - - -
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Residues in contact with VAL 55 (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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51A ARG* 3.1 22.6 + - + +
52A HIS* 3.2 18.1 + - + +
54A LYS* 1.3 77.0 - - + +
56A HIS* 1.3 62.1 + - + +
58A GLY* 3.1 10.9 + - - -
60A PRO* 5.5 0.9 - - - +
70A VAL* 3.4 43.2 - - + +
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Residues in contact with HIS 56 (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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34A CYS* 3.9 0.2 - - - -
36A HIS* 3.4 49.1 + + + +
39A CYS* 3.7 7.8 - - + -
52A HIS* 3.2 34.1 + + - -
53A GLU* 3.2 10.7 + - - +
55A VAL* 1.3 77.7 - - + +
57A ALA* 1.3 59.7 + - - +
58A GLY 3.4 6.2 + - - +
60A PRO* 5.6 1.2 - - - +
1087A ZN 2.1 36.6 - - - -
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Residues in contact with ALA 57 (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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53A GLU 3.3 7.7 + - - +
54A LYS* 3.1 13.8 + - - +
56A HIS* 1.3 77.2 - - - +
58A GLY* 1.3 63.9 + - - +
59A TYR* 4.9 8.1 - - - -
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Residues in contact with GLY 58 (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 LYS 3.3 6.0 + - - -
55A VAL* 3.1 11.3 + - - -
56A HIS 3.8 5.2 - - - +
57A ALA* 1.3 84.2 - - - +
59A TYR* 1.3 71.2 + - - -
60A PRO* 3.4 12.2 - - - +
70A VAL* 4.0 5.6 - - - -
71A GLY 3.3 12.1 - - - -
72A LYS* 5.0 5.8 - - - -
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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