Contacts of the helix formed by residues 53 - 66 (chain A) in PDB entry 4EJJ
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 GLN 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASN* 2.9 26.0 + - - +
52A GLU* 1.3 98.9 + - + +
54A MET* 1.3 54.8 + - - +
55A TYR 3.3 2.2 - - - -
56A ASN* 3.2 36.6 + - + +
57A SER* 2.8 35.1 + - - +
478A VAL* 4.8 5.2 - - - -
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Residues in contact with MET 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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49A LEU* 4.0 20.0 - - + -
50A ASN 3.7 8.5 - - - +
51A THR* 4.2 5.1 + - - +
52A GLU 3.8 1.6 - - - -
53A GLN* 1.3 71.1 - - - +
55A TYR* 1.3 61.0 + - - +
57A SER* 3.2 4.2 + - - -
58A LEU* 2.9 58.7 + - + +
73A LEU* 3.7 29.6 - - + -
218A GLN* 3.4 43.5 - - + +
222A MET* 3.9 25.4 - - - -
368A MET* 4.3 12.6 - - + -
392A TYR* 5.2 0.7 - - + -
478A VAL* 4.7 4.0 + - - +
479A GLY* 5.1 4.9 - - - -
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Residues in contact with TYR 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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53A GLN 3.3 0.4 - - - -
54A MET* 1.3 78.0 - - - +
56A ASN* 1.3 82.2 + - - +
58A LEU* 3.4 1.4 + - - +
59A MET* 3.0 44.7 + - + +
367A PRO* 4.1 17.9 - - + -
368A MET* 4.4 9.7 - - + -
394A MET* 3.7 29.6 - - + -
396A GLY* 3.3 14.5 + - - -
397A SER* 3.2 38.6 + - - -
400A ARG* 3.3 30.4 + - - +
478A VAL* 4.6 21.7 - - + +
479A GLY* 6.1 0.4 - - - +
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Residues in contact with ASN 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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53A GLN* 3.2 41.7 + - + +
54A MET 3.3 0.4 - - - -
55A TYR* 1.3 96.1 - - - +
57A SER* 1.3 52.3 - - - +
59A MET* 3.5 5.2 + - - +
60A LYS* 2.9 33.1 + - - +
478A VAL* 6.4 0.2 - - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN 4.3 4.8 + - - +
49A LEU* 4.1 17.3 - - - -
50A ASN* 2.9 36.1 + - - +
53A GLN* 2.8 24.5 + - - +
54A MET* 3.3 7.9 - - - -
56A ASN* 1.3 72.7 - - - +
58A LEU* 1.3 64.6 + - - +
60A LYS* 3.3 7.8 + - - +
61A ILE* 3.1 28.6 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.9 13.9 - - + -
54A MET* 2.9 38.7 + - + +
57A SER* 1.3 72.7 - - - +
59A MET* 1.3 58.2 + - - +
61A ILE* 3.2 3.3 + - + +
62A SER* 3.0 22.7 + - - -
69A PHE* 3.3 28.4 - - + -
71A ILE* 3.8 39.0 - - + -
73A LEU* 5.5 0.2 - - + -
80A VAL* 4.4 4.9 - - + -
82A CYS* 5.5 0.2 - - - -
368A MET* 3.9 24.0 - - - -
392A TYR* 4.0 15.7 - - + -
394A MET* 3.9 20.9 - - + -
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Residues in contact with MET 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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55A TYR* 3.0 48.9 + - + +
56A ASN* 3.8 6.1 - - - +
58A LEU* 1.3 72.3 - - - +
60A LYS* 1.3 67.9 + - - +
62A SER* 2.5 31.3 + - - +
63A GLU* 3.0 17.6 + - + +
82A CYS* 4.0 22.2 - - + -
394A MET* 4.7 5.2 - - - -
397A SER* 3.7 31.9 - - - -
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Residues in contact with LYS 60 (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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56A ASN 2.9 18.7 + - - +
57A SER* 3.3 7.4 + - - +
59A MET* 1.3 76.8 - - - +
61A ILE* 1.3 65.3 + - + +
63A GLU* 3.4 45.4 + - - +
64A ARG* 3.6 8.1 + - - +
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Residues in contact with ILE 61 (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 PRO* 4.0 10.8 - - + -
48A GLN* 4.0 32.8 - - + +
49A LEU* 4.4 7.0 - - + -
57A SER 3.1 18.3 + - - +
58A LEU* 3.2 8.5 + - - +
59A MET 3.1 0.2 - - - -
60A LYS* 1.3 80.2 - - + +
62A SER* 1.3 50.5 + - - +
64A ARG* 3.1 5.0 + - - -
65A TYR* 2.8 52.6 + - + +
69A PHE* 3.5 29.2 - - + -
71A ILE* 3.8 23.8 - - + -
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Residues in contact with SER 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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58A LEU 3.0 11.2 + - - -
59A MET* 2.5 39.7 + - - +
61A ILE* 1.3 73.0 - - - +
63A GLU* 1.3 62.2 + - - +
64A ARG 3.1 0.2 - - - -
66A GLY* 2.8 47.9 + - - +
67A PRO* 4.9 1.1 - - - -
69A PHE* 3.7 13.4 - - - -
82A CYS* 4.0 15.0 - - - -
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Residues in contact with GLU 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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59A MET* 3.0 18.2 + - + +
60A LYS* 3.5 40.8 + - - +
61A ILE 3.3 0.4 - - - -
62A SER* 1.3 84.2 + - - +
64A ARG* 1.3 57.5 + - - +
66A GLY 5.1 0.2 + - - -
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Residues in contact with ARG 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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60A LYS* 3.6 8.6 + - - +
61A ILE* 3.1 8.7 + - - +
62A SER 3.1 0.8 - - - -
63A GLU* 1.3 81.6 - - - +
65A TYR* 1.3 101.4 + - + +
66A GLY 3.6 0.6 + - - -
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Residues in contact with TYR 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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35A PRO* 3.7 28.5 - - + +
36A GLY* 3.5 28.0 + - - -
37A PRO* 3.1 43.1 - - + +
61A ILE* 2.8 38.1 + - + +
64A ARG* 1.3 118.2 + - + +
66A GLY* 1.3 57.4 + - - +
68A VAL 4.4 2.1 - - - +
69A PHE* 4.0 19.3 - - + -
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Residues in contact with GLY 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 SER* 2.8 36.5 + - - +
63A GLU 4.8 0.4 - - - -
64A ARG 3.6 1.2 - - - -
65A TYR* 1.3 76.6 - - - +
67A PRO* 1.4 73.7 - - - +
68A VAL 3.3 4.8 + - - +
69A PHE* 3.6 7.3 - - - -
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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