Contacts of the helix formed by residues 47 - 60 (chain A) in PDB entry 1EJC
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 4.0 24.9 - - + -
45A PRO* 3.2 32.8 + - + -
46A LYS* 1.3 83.2 - - - +
48A LYS* 1.3 67.2 + - - +
49A ASP 3.4 0.2 - - - -
50A ILE* 2.9 22.2 + - + +
51A ASP* 3.4 10.2 + - - +
396A ASP 3.3 24.2 - - - +
397A ARG 3.7 20.0 - - - +
398A GLY 4.0 15.0 - - - +
399A TYR 3.5 21.3 - - - +
400A GLU* 3.9 6.1 - - - +
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Residues in contact with LYS 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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47A LEU* 1.3 72.4 - - - +
49A ASP* 1.3 67.9 + - - +
51A ASP* 2.9 24.9 + - + +
52A THR* 2.9 25.9 + - - +
89A THR* 4.6 23.4 - - - +
396A ASP 5.2 0.8 + - - -
397A ARG* 3.3 60.3 + - + +
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Residues in contact with ASP 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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22A LYS* 3.3 37.7 + - + +
26A LEU* 4.1 12.9 - - + +
47A LEU* 3.4 2.4 - - - +
48A LYS* 1.3 81.0 - - - +
50A ILE* 1.3 56.7 + - - +
52A THR* 4.1 4.5 + - - -
53A THR* 2.9 34.0 + - - -
89A THR* 4.3 7.3 + - - +
90A MET* 3.6 35.2 - - - +
397A ARG* 5.4 5.5 + - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 4.3 10.5 - - + -
25A ALA* 4.1 12.6 - - + -
26A LEU* 3.9 18.8 - - + -
29A LEU* 3.9 13.7 - - + -
44A VAL* 3.7 20.0 - - + -
45A PRO* 3.4 22.2 - - + +
47A LEU* 2.9 20.1 + - + +
49A ASP* 1.3 76.2 - - - +
51A ASP* 1.3 59.7 + - - +
53A THR* 3.3 6.6 + - - -
54A MET* 2.9 34.8 + - - +
66A ARG* 3.6 24.0 - - - +
70A VAL* 4.3 10.1 - - + -
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Residues in contact with ASP 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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46A LYS* 5.8 0.9 - - - -
47A LEU 3.9 13.2 + - - +
48A LYS* 2.9 15.0 + - + +
50A ILE* 1.3 76.0 - - - +
52A THR* 1.3 65.7 + - - +
54A MET* 3.2 11.2 + - - +
55A LYS* 3.0 39.6 + - - +
66A ARG* 4.4 17.7 + - - -
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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 LYS* 2.9 26.1 + - - +
49A ASP* 3.7 9.9 + - - -
51A ASP* 1.3 76.0 - - - +
53A THR* 1.3 62.1 + - - +
55A LYS* 3.3 10.7 + - + +
56A LEU* 3.0 21.8 + - - +
86A LEU* 3.6 22.6 - - - +
89A THR* 3.8 23.8 + - - +
90A MET* 4.1 21.1 - - + -
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Residues in contact with THR 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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26A LEU* 3.2 18.0 - - + +
29A LEU* 3.8 33.2 - - + -
30A PHE* 3.8 20.1 - - + -
49A ASP 2.9 23.3 + - - -
50A ILE 3.5 4.5 - - - -
51A ASP 3.2 0.2 - - - -
52A THR* 1.3 75.6 - - - +
54A MET* 1.3 60.8 + - - +
56A LEU* 3.1 5.1 + - - +
57A LEU* 2.9 38.3 + - + +
90A MET* 3.3 18.5 - - - +
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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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29A LEU* 5.5 2.9 - - + -
50A ILE* 2.9 26.1 + - + +
51A ASP* 3.2 13.4 + - - +
53A THR* 1.3 77.5 - - + +
55A LYS* 1.3 62.4 + - + +
57A LEU* 3.4 7.2 + - + +
58A THR* 2.9 30.4 + - - -
64A VAL* 3.5 36.5 - - + +
65A GLU* 3.6 27.8 - - - +
66A ARG* 3.7 31.9 - - + +
70A VAL* 4.3 10.8 - - + -
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Residues in contact with LYS 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 ASP* 3.0 27.9 + - - +
52A THR* 3.7 10.8 - - + +
54A MET* 1.3 77.8 - - + +
56A LEU* 1.3 63.0 + - - +
58A THR* 3.5 7.5 + - - -
59A GLN* 3.2 20.6 + - - +
86A LEU* 4.0 20.0 - - + +
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Residues in contact with LEU 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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30A PHE* 3.9 24.7 - - + -
52A THR 3.0 13.6 + - - +
53A THR* 3.1 7.8 + - - +
55A LYS* 1.3 75.2 - - - +
57A LEU* 1.3 66.2 + - - +
59A GLN* 3.1 14.3 + - + +
60A LEU* 3.2 31.6 + - + +
82A ALA* 3.8 23.8 - - + -
83A PRO* 5.2 0.7 - - + -
86A LEU* 4.2 24.4 - - + +
87A VAL* 4.1 8.3 - - + -
90A MET* 4.5 5.4 - - + -
93A SER* 3.9 28.7 - - - +
96A ALA* 5.0 1.3 - - + -
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Residues in contact with LEU 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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29A LEU* 3.8 24.5 - - + +
30A PHE* 4.5 14.1 - - + -
33A LEU* 3.7 38.1 - - + -
53A THR* 2.9 33.5 + - + +
54A MET* 3.8 5.4 - - - +
56A LEU* 1.3 75.6 - - - +
58A THR* 1.3 61.6 + - - +
60A LEU* 3.0 14.6 + - + +
62A THR* 2.8 37.0 + - + +
64A VAL* 4.1 4.7 - - + -
72A ILE* 3.9 27.4 - - + -
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Residues in contact with THR 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 MET 2.9 19.0 + - - -
55A LYS* 3.7 8.0 - - - -
56A LEU 3.2 0.2 - - - -
57A LEU* 1.3 77.8 - - - +
59A GLN* 1.3 57.6 + - - +
61A GLY* 2.9 21.3 + - - -
62A THR* 3.3 16.0 + - - +
64A VAL* 3.8 17.7 + - - +
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Residues in contact with GLN 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 LYS 3.2 3.7 + - - +
56A LEU 3.1 10.7 + - - +
58A THR* 1.3 79.4 - - - +
60A LEU* 1.3 61.1 + - + +
61A GLY 3.2 1.0 + - - -
79A ASN* 2.9 33.0 + - - +
81A SER 4.5 1.1 - - - +
83A PRO* 3.7 25.2 - - + +
86A LEU* 3.4 30.6 - - + +
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Residues in contact with LEU 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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33A LEU* 3.9 32.3 - - + -
56A LEU* 3.4 30.1 - - + +
57A LEU* 3.0 13.7 + - + +
59A GLN* 1.3 77.2 - - + +
61A GLY* 1.3 58.9 + - - +
62A THR* 4.4 2.2 - - - +
77A VAL* 3.1 13.3 - - + +
78A ASN 3.0 21.7 + - - -
79A ASN* 3.1 30.1 + - - +
80A PHE* 4.3 2.7 - - - -
81A SER 3.5 33.7 - - - +
82A ALA* 4.3 0.9 - - - +
96A ALA* 4.6 3.8 - - + -
100A LEU* 4.3 13.7 - - + -
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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