Contacts of the helix formed by residues 49 - 59 (chain A) in PDB entry 4JYY
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 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.4 11.0 - - - +
46A PRO 5.3 0.4 + - - -
48A ILE* 1.3 76.0 - - - +
50A LYS* 1.3 65.9 + - - +
51A GLU* 3.8 11.2 + - + +
52A THR* 2.7 47.9 + - - +
53A MET* 3.1 20.7 + - - +
199A TYR* 6.0 0.7 - - - -
201A LEU* 4.0 7.9 - - - +
202A LYS* 3.3 35.9 - - + +
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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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41A TYR* 3.3 33.7 - - + +
42A ASP* 3.9 21.4 - - + +
45A GLU* 2.8 18.4 + - - +
48A ILE 3.8 0.8 + - - -
49A ASP* 1.3 70.2 - - - +
51A GLU* 1.3 66.0 + - - +
53A MET* 3.3 1.9 + - - +
54A LYS* 2.9 49.6 + - + +
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Residues in contact with GLU 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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49A ASP* 3.3 9.3 - - + +
50A LYS* 1.3 78.9 - - - +
52A THR* 1.3 57.7 + - - +
54A LYS* 3.3 7.6 + - - +
55A LEU* 3.0 38.3 + - + +
201A LEU* 3.7 26.5 - - + +
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Residues in contact with THR 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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48A ILE* 4.2 11.4 - - + -
49A ASP* 2.7 38.2 + - - +
50A LYS 3.2 0.4 - - - -
51A GLU* 1.3 74.1 - - - +
53A MET* 1.3 56.5 + - - +
55A LEU* 3.7 5.3 - - - +
56A HIS* 2.7 47.6 + - + +
197A HIS 3.8 16.2 + - - +
198A ALA* 3.6 26.4 - - - +
199A TYR* 5.3 1.7 - - - -
201A LEU* 3.6 23.4 + - - +
202A LYS 4.9 0.2 + - - -
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Residues in contact with MET 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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37A LEU* 4.7 5.6 - - + -
39A TYR* 5.2 4.9 - - + -
41A TYR* 3.4 39.3 - - + +
44A LEU* 2.9 40.4 - - + -
48A ILE* 3.0 45.5 - - + +
49A ASP 3.1 13.3 + - - +
50A LYS 3.6 2.7 - - - +
52A THR* 1.3 75.8 - - - +
54A LYS* 1.3 58.6 + - - +
56A HIS* 3.9 6.4 - - - +
57A HIS* 2.9 34.3 + - - +
114A PHE* 6.3 0.4 - - - -
115A PHE* 4.7 14.6 - - - -
118A MET* 4.2 8.5 - - + -
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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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41A TYR* 3.6 42.0 - - + -
50A LYS* 2.9 43.3 + - + +
51A GLU* 3.5 9.9 - - + +
53A MET* 1.3 74.1 - - - +
55A LEU* 1.3 61.4 + - + +
58A ASP* 2.8 49.6 + - - +
59A LYS* 4.7 0.2 - - - +
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Residues in contact with LEU 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 GLU* 3.0 28.7 + - + +
52A THR* 3.7 4.0 - - - +
54A LYS* 1.3 77.8 - - + +
56A HIS* 1.3 61.1 + - - +
59A LYS* 2.8 49.0 + - + +
60A HIS* 3.1 21.0 + - + +
197A HIS 6.2 0.2 - - - +
201A LEU* 3.7 30.1 - - + -
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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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52A THR* 2.7 31.6 + - + +
53A MET* 3.9 5.9 - - - +
55A LEU* 1.3 75.5 - - - +
57A HIS* 1.3 57.3 + - - +
60A HIS* 3.5 7.9 - - + +
61A TYR* 3.0 27.9 + - - +
111A HIS* 3.2 12.9 + + - -
114A PHE* 3.7 27.4 - + - -
115A PHE* 3.8 16.6 - + + -
193A ASP* 2.9 13.4 + - - -
197A HIS* 3.5 15.7 + + - +
198A ALA* 3.9 18.4 + - + -
301A FE 2.3 29.7 - - - -
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Residues in contact with HIS 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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34A VAL* 3.5 23.8 - - + +
35A LYS 2.7 26.5 + - - -
36A PRO* 4.3 4.3 - - + -
37A LEU* 3.3 34.6 + - + -
41A TYR* 3.5 15.3 + - + -
53A MET 2.9 17.7 + - - +
56A HIS* 1.3 78.3 - - - +
58A ASP* 1.3 85.5 + - - +
61A TYR* 3.3 31.9 - + - +
62A GLN* 3.4 7.4 + - - +
115A PHE* 3.7 18.4 - + + -
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Residues in contact with ASP 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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41A TYR* 2.7 37.0 + - - -
54A LYS* 2.8 38.0 + - - +
57A HIS* 1.3 94.5 + - - +
59A LYS* 1.3 70.5 + - + +
62A GLN* 3.1 23.1 - - - +
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Residues in contact with LYS 59 (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 4.7 0.4 - - - +
55A LEU* 2.8 38.7 + - + +
58A ASP* 1.3 90.6 + - + +
60A HIS* 1.3 65.7 + - + +
61A TYR 3.5 0.2 - - - -
62A GLN* 3.7 1.4 - - - +
63A ALA* 2.9 31.4 + - - +
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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