Contacts of the helix formed by residues 47 - 60 (chain B) in PDB entry 1EJD
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LYS* 3.9 23.6 - - + +
45B PRO* 3.4 32.4 + - + -
46B LYS* 1.3 83.4 - - - +
48B LYS* 1.3 66.4 + - - +
49B ASP 3.3 3.1 - - - +
50B ILE* 2.9 22.3 + - + +
51B ASP* 3.2 16.5 + - - -
396B ASP 3.4 25.4 - - - +
397B ARG 3.8 18.8 - - - +
398B GLY 4.3 9.9 - - - +
399B TYR 3.5 21.5 - - - +
400B GLU* 3.9 5.6 - - - +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 1.3 71.8 - - - +
49B ASP* 1.3 64.1 + - - +
51B ASP* 2.9 14.8 + - + +
52B THR* 2.9 35.2 + - - +
89B THR* 3.7 25.0 + - - -
396B ASP 5.3 0.8 + - - -
397B ARG* 2.9 70.0 + - + +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.1 35.0 + - + +
26B LEU* 4.1 18.5 - - + +
47B LEU* 3.3 2.0 - - - +
48B LYS* 1.3 86.6 - - - +
50B ILE* 1.3 56.9 + - - +
52B THR* 3.7 4.3 + - - -
53B THR* 2.8 33.3 + - - -
89B THR* 4.3 6.9 + - - +
90B MET* 3.5 34.7 - - - +
397B ARG* 5.4 4.0 + - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 4.4 8.5 - - + -
25B ALA* 3.9 25.6 - - + -
26B LEU* 3.9 21.3 - - + -
29B LEU* 4.0 14.4 - - + -
44B VAL* 3.7 12.1 - - + -
45B PRO* 3.4 20.6 - - + +
47B LEU* 2.9 20.3 + - + +
49B ASP* 1.3 77.1 - - - +
51B ASP* 1.3 58.7 + - - +
53B THR* 3.3 5.0 + - - -
54B MET* 2.9 40.0 + - + +
66B ARG* 3.7 23.1 - - - +
70B VAL* 4.6 0.7 - - + -
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Residues in contact with ASP 51 (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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46B LYS* 5.8 1.4 - - - -
47B LEU 3.2 14.0 + - - +
48B LYS* 2.9 14.6 + - + +
50B ILE* 1.3 78.4 - - - +
52B THR* 1.3 62.1 + - - +
54B MET* 3.3 25.6 + - + +
55B LYS* 3.0 39.8 + - - +
66B ARG* 4.9 4.9 + - - -
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 2.9 23.5 + - - +
49B ASP* 3.7 9.0 + - - -
51B ASP* 1.3 75.4 - - - +
53B THR* 1.3 57.8 + - - +
55B LYS* 3.2 20.2 + - + +
56B LEU* 2.9 27.2 + - - +
86B LEU* 3.5 24.4 - - - +
89B THR* 4.0 25.0 + - + +
90B MET* 3.9 23.8 - - + -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.1 18.9 - - + +
29B LEU* 3.9 30.5 - - + -
30B PHE* 3.8 23.7 - - + -
49B ASP 2.8 21.3 + - - -
50B ILE* 3.5 5.6 - - - -
51B ASP 3.3 0.2 - - - -
52B THR* 1.3 75.3 - - - +
54B MET* 1.3 61.4 + - - +
56B LEU* 3.2 4.7 + - - +
57B LEU* 2.8 42.8 + - + +
90B MET* 3.3 16.6 - - - +
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Residues in contact with MET 54 (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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29B LEU* 5.5 3.6 - - + -
50B ILE* 2.9 22.4 + - + +
51B ASP* 3.3 35.0 + - - +
53B THR* 1.3 76.2 - - + +
55B LYS* 1.3 57.5 + - + +
57B LEU* 3.4 6.9 + - + +
58B THR* 2.9 34.2 + - - +
64B VAL* 3.8 30.5 - - + +
65B GLU* 5.6 0.2 - - - -
66B ARG* 3.7 42.4 - - + -
70B VAL* 4.3 13.0 - - + -
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Residues in contact with LYS 55 (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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51B ASP* 3.0 40.0 + - - +
52B THR* 3.5 18.8 + - + +
53B THR 3.2 0.2 - - - -
54B MET* 1.3 74.0 - - + +
56B LEU* 1.3 67.0 + - - +
58B THR* 3.3 7.5 + - - -
59B GLN* 3.0 23.4 + - - +
86B LEU* 4.5 20.1 - - + +
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Residues in contact with LEU 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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30B PHE* 4.0 30.3 - - + -
52B THR 2.9 16.9 + - - +
53B THR* 3.2 5.1 + - - +
55B LYS* 1.3 76.5 - - - +
57B LEU* 1.3 65.0 + - + +
59B GLN* 3.2 12.1 + - - +
60B LEU* 3.3 32.5 + - + +
82B ALA* 4.2 18.2 - - + -
83B PRO* 5.7 0.2 - - + -
86B LEU* 4.5 21.9 - - + +
87B VAL* 4.2 12.8 - - + -
90B MET* 4.5 5.6 - - + -
93B SER* 3.9 29.4 - - - +
96B ALA* 4.4 6.7 - - + -
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Residues in contact with LEU 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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29B LEU* 3.9 20.0 - - + +
30B PHE* 4.3 15.3 - - + -
33B LEU* 3.8 40.2 - - + -
53B THR* 2.8 36.3 + - + +
54B MET* 3.8 7.0 - - + +
56B LEU* 1.3 77.2 - - + +
58B THR* 1.3 62.3 + - - +
60B LEU* 3.0 16.9 + - + +
62B THR* 2.9 30.5 + - + +
64B VAL* 3.9 13.9 - - + -
72B ILE* 4.1 20.2 - - + -
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Residues in contact with THR 58 (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 MET* 2.9 19.3 + - - +
55B LYS* 3.6 7.9 - - - -
56B LEU 3.2 0.2 - - - -
57B LEU* 1.3 77.4 - - - +
59B GLN* 1.3 58.3 + - - +
61B GLY* 2.9 20.3 + - - -
62B THR 3.5 13.9 + - - +
64B VAL* 3.8 19.1 + - - +
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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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55B LYS 3.0 13.6 + - - +
56B LEU 3.2 9.3 + - - +
58B THR* 1.3 76.2 - - - +
60B LEU* 1.3 59.5 + - + +
61B GLY 3.2 0.4 + - - -
78B ASN* 5.4 0.2 - - - +
79B ASN* 3.0 28.4 + - - +
81B SER 5.1 0.9 - - - +
83B PRO* 4.8 10.1 - - + -
86B LEU* 3.8 24.3 - - + +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 35.9 - - + -
56B LEU* 3.4 32.8 - - + +
57B LEU* 3.0 12.1 + - + +
59B GLN* 1.3 78.3 - - - +
61B GLY* 1.3 58.3 + - - +
62B THR* 3.6 2.5 - - - +
77B VAL* 3.4 9.1 - - + +
78B ASN* 3.0 23.8 + - - +
79B ASN* 3.1 31.1 + - - +
80B PHE* 4.2 3.4 - - - -
81B SER 3.7 32.1 - - - +
82B ALA* 4.7 0.7 - - + +
96B ALA* 5.0 0.4 - - + -
100B LEU* 4.3 15.9 - - + -
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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