Contacts of the helix formed by residues 41 - 59 (chain C) in PDB entry 4KEU
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 ASN 41 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 4.4 0.4 + - - -
40C TYR* 1.3 75.3 - - - +
42C GLU* 1.3 61.2 + - - +
43C ASP* 3.0 24.3 + - - +
44C GLU* 3.0 43.5 + - + +
45C GLU* 3.2 26.4 + - - +
47C ARG* 5.2 1.2 - - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 4.1 16.6 + - - +
33C ARG* 4.0 9.8 + - - +
40C TYR 4.0 1.2 + - - -
41C ASN* 1.3 73.2 + - - +
43C ASP* 1.3 60.4 + - - +
45C GLU* 3.3 12.5 + - - +
46C PHE* 2.9 30.3 + - + +
75C ASP* 5.7 0.3 - - - +
78C PHE* 4.1 20.4 - - + +
81C LYS* 4.2 18.3 + - - +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASN* 3.0 10.0 + - - +
42C GLU* 1.3 79.6 - - - +
44C GLU* 1.3 57.5 + - - +
46C PHE* 3.4 6.9 + - - +
47C ARG* 2.9 50.8 + - - +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASN* 3.0 39.7 + - - +
43C ASP* 1.3 73.6 - - - +
45C GLU* 1.3 62.0 + - + +
47C ARG* 3.4 25.6 + - - +
48C ASN* 2.8 45.7 + - - +
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 5.0 1.6 - - - +
26C ARG* 2.7 47.4 + - + -
33C ARG* 2.8 30.6 + - - -
40C TYR* 3.7 14.9 - - - +
41C ASN 3.3 14.5 + - - +
42C GLU* 3.3 9.0 - - - +
44C GLU* 1.3 79.2 - - + +
46C PHE* 1.3 61.4 - - - +
48C ASN* 3.9 1.4 - - - +
49C ALA* 3.0 26.0 + - - +
78C PHE* 3.7 6.1 - - + -
260C THR* 3.7 37.9 + - + +
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Residues in contact with PHE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 2.9 19.9 + - + +
43C ASP* 3.7 5.4 - - - +
45C GLU* 1.3 76.7 - - - +
47C ARG* 1.3 69.9 + - + +
49C ALA* 3.3 2.3 + - - +
50C VAL* 3.0 50.9 + - + +
78C PHE* 3.7 19.4 - + + -
81C LYS* 3.6 42.8 - - + -
82C VAL* 3.9 11.7 - - + -
85C ALA* 3.9 16.4 - - + -
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASN* 5.2 1.0 - - - +
43C ASP* 2.9 31.5 + - - +
44C GLU* 3.8 36.4 + - - +
46C PHE* 1.3 83.1 - - + +
48C ASN* 1.3 69.2 + - - +
50C VAL* 3.9 3.1 - - - +
51C ASN* 3.0 38.9 + - - +
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 2.8 35.2 + - - +
45C GLU 3.9 3.1 - - - +
47C ARG* 1.3 78.0 + - - +
49C ALA* 1.3 61.7 + - - +
51C ASN* 3.8 6.8 - - - +
52C GLU* 3.0 31.8 + - + +
259C CYS* 3.8 20.6 + - + +
260C THR* 3.8 13.4 + - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.9 26.0 - - + +
45C GLU 3.0 17.7 + - - +
46C PHE 3.8 3.4 - - - +
48C ASN* 1.3 73.4 - - - +
50C VAL* 1.3 67.7 + - - +
52C GLU* 3.5 1.0 + - - +
53C VAL* 2.9 31.2 + - - +
78C PHE* 4.2 5.8 - - + -
82C VAL* 4.1 20.2 - - + -
259C CYS* 3.9 12.7 - - + +
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.0 56.1 + - + +
47C ARG* 3.9 4.9 - - - +
49C ALA* 1.3 77.1 - - - +
51C ASN* 1.3 61.4 + - - +
53C VAL* 3.4 1.3 + - - +
54C LYS* 2.9 54.9 + - + +
82C VAL* 4.7 6.5 - - + -
85C ALA* 4.0 12.8 - - + +
86C THR* 3.8 22.0 - - + -
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ARG* 3.0 30.9 + - - +
48C ASN* 3.8 7.3 - - - +
50C VAL* 1.3 85.1 - - - +
52C GLU* 1.3 66.4 + - - +
54C LYS* 3.4 10.2 + - - +
55C ARG* 3.0 26.5 + - - +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 3.0 23.3 + - + +
49C ALA 3.9 0.2 - - - +
51C ASN* 1.3 78.1 - - - +
53C VAL* 1.3 63.0 + - - +
55C ARG* 2.6 45.6 + - - +
56C ALA 2.9 18.4 + - - -
257C TYR* 3.5 27.7 + - + +
259C CYS* 3.8 19.1 - - + -
279C SER* 3.7 2.9 - - - -
280C ILE* 3.2 38.2 + - + +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.6 27.6 - - + -
49C ALA 2.9 22.9 + - - +
50C VAL 3.9 2.5 - - - +
52C GLU* 1.3 76.1 - - + +
54C LYS* 1.3 57.4 + - - +
56C ALA* 3.2 7.6 + - - +
57C MET* 2.9 29.4 + - - +
64C ILE* 4.1 15.3 - - + -
82C VAL* 4.3 6.1 - - + -
86C THR* 3.7 19.7 - - + +
88C ILE* 3.6 37.5 - - + -
280C ILE* 4.8 4.0 - - + -
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 2.9 33.0 + - + +
51C ASN* 3.8 10.9 - - - +
53C VAL* 1.3 76.4 - - - +
55C ARG* 1.3 61.9 + - - +
57C MET* 3.2 11.6 + - - +
58C GLN* 3.0 28.1 + - + +
85C ALA* 3.5 24.5 + - - +
86C THR* 4.2 13.2 - - + +
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ASN* 3.0 15.2 + - - +
52C GLU* 2.6 48.3 + - - +
54C LYS* 1.3 75.7 - - - +
56C ALA* 1.3 61.6 + - - +
58C GLN* 3.3 29.7 + - - +
59C PHE* 3.4 25.6 + - + -
279C SER* 3.1 18.8 + - - -
280C ILE* 4.6 0.2 - - - -
281C THR* 2.8 36.4 + - + +
285C GLU* 4.3 3.6 + - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 4.8 0.9 - - + -
52C GLU 2.9 13.3 + - - +
53C VAL* 3.4 12.6 - - - +
54C LYS 3.2 0.2 - - - -
55C ARG* 1.3 79.3 - - - +
57C MET* 1.3 59.7 + - + +
59C PHE* 3.1 12.1 + - - +
61C VAL* 3.2 40.9 + - + +
64C ILE* 4.8 2.9 - - + -
280C ILE* 4.0 25.1 - - + +
281C THR* 3.8 10.5 - - + +
284C PHE* 5.4 0.2 - - - -
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Residues in contact with MET 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 2.9 24.4 + - - +
54C LYS* 3.2 11.6 + - - +
56C ALA* 1.3 73.6 - - - +
58C GLN* 1.3 61.4 + - + +
60C GLY* 2.9 19.4 + - - -
61C VAL 3.7 13.1 + - - +
62C LYS* 5.5 2.9 + - - -
86C THR* 3.2 31.6 - - - +
87C GLY 4.0 5.4 - - - +
88C ILE* 3.7 44.9 - - + +
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Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS* 3.0 18.1 + - - +
55C ARG* 3.4 27.6 - - - +
56C ALA 3.2 0.2 - - - -
57C MET* 1.3 76.7 - - - +
59C PHE* 1.3 62.7 + - + +
60C GLY 3.2 1.2 + - - -
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 5.8 1.6 - - - -
55C ARG* 3.4 29.8 + - + -
56C ALA 3.1 9.6 + - - +
57C MET 3.1 1.2 - - - -
58C GLN* 1.3 78.0 - - + +
60C GLY* 1.3 58.7 + - - +
61C VAL 3.6 1.3 - - - -
281C THR* 3.5 33.4 - - + -
284C PHE* 3.6 56.1 - + + -
285C GLU* 4.4 15.3 - - + -
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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
------------------------------------------------------------
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