Contacts of the helix formed by residues 53 - 69 (chain C) in PDB entry 5HK1
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 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C LEU* 1.3 71.4 - - - +
54C HIS* 1.3 71.3 + - - +
55C GLU* 3.0 33.4 + - - +
56C LEU* 2.8 35.4 + - + +
57C ALA* 2.8 11.7 + - - -
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Residues in contact with HIS 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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141A THR* 3.1 39.4 + - - -
142A LYS* 6.3 0.4 - - + -
52C LEU 3.3 5.7 + - - -
53C ASP* 1.3 82.9 + - - +
55C GLU* 1.3 80.8 + - + +
57C ALA* 4.2 7.2 - - - -
58C PHE* 2.9 44.9 + + + -
129C ILE* 4.2 5.4 - - + -
130C SER* 4.0 9.9 + - - +
167C ASN* 5.1 6.2 - - + +
169C TRP* 3.6 52.4 + + + -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 3.2 29.7 + - - +
53C ASP* 3.0 18.8 + - - +
54C HIS* 1.3 92.0 - - + +
56C LEU* 1.3 58.8 + - - +
58C PHE* 3.8 8.6 - - - +
59C SER* 3.2 23.9 + - - -
81C TRP* 5.3 2.6 + - - -
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Residues in contact with LEU 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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52C LEU* 4.3 19.1 - - + -
53C ASP* 2.8 26.1 + - + +
55C GLU* 1.3 73.2 - - - +
57C ALA* 1.3 63.0 + - - +
59C SER* 2.7 24.8 + - - +
60C ARG* 3.1 59.5 + - + +
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Residues in contact with ALA 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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49C TYR* 3.3 40.3 - - + +
52C LEU* 4.4 8.0 - - + +
53C ASP 2.8 12.6 + - - +
54C HIS 3.8 2.0 - - - +
56C LEU* 1.3 78.0 - - - +
58C PHE* 1.3 63.4 + - + +
60C ARG* 4.0 0.8 - - - -
61C LEU* 3.0 26.4 + - - +
129C ILE* 3.6 26.5 - - + -
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Residues in contact with PHE 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 HIS* 2.9 34.0 + + + +
55C GLU* 3.8 9.6 - - - +
57C ALA* 1.3 79.4 - - + +
59C SER* 1.3 62.8 + - - +
61C LEU* 3.3 4.7 + - + +
62C ILE* 3.0 33.1 + - + +
81C TRP* 3.8 29.2 - + - -
106C LEU* 3.5 47.1 - - + +
107C PHE 4.7 0.4 - - - -
129C ILE* 4.1 25.4 - - + -
169C TRP* 3.7 35.4 - + + -
170C MET 4.3 7.6 - - - -
171C VAL* 4.5 2.0 - - + -
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Residues in contact with SER 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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55C GLU 3.2 12.4 + - - -
56C LEU* 2.7 31.4 + - - +
58C PHE* 1.3 80.0 - - - +
60C ARG* 1.3 62.7 + - - +
62C ILE* 3.5 8.1 + - - +
63C VAL* 3.3 29.3 + - - +
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Residues in contact with ARG 60 (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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49C TYR* 3.6 32.2 + - + -
52C LEU* 3.9 20.2 - - - +
56C LEU* 3.1 50.9 + - + +
59C SER* 1.3 80.1 + - - +
61C LEU* 1.3 60.0 + - - +
63C VAL* 3.5 6.6 + - - +
64C GLU* 3.0 28.2 + - - +
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Residues in contact with LEU 61 (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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42C ILE* 5.5 2.0 - - + +
45C LEU* 3.9 30.5 - - + +
46C ALA* 4.4 4.7 - - + +
49C TYR* 3.7 30.5 - - + -
57C ALA 3.0 19.8 + - - +
58C PHE* 3.7 5.6 - - + +
60C ARG* 1.3 75.5 - - - +
62C ILE* 1.3 59.6 + - - +
64C GLU* 3.1 3.5 + - - +
65C LEU* 2.8 44.3 + - + +
96C LEU* 5.0 1.1 - - + -
106C LEU* 4.1 13.2 - - + -
129C ILE* 6.0 0.4 - - + -
171C VAL* 3.5 41.5 - - + -
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Residues in contact with ILE 62 (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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58C PHE* 3.0 19.2 + - + +
59C SER* 3.9 7.4 - - - +
61C LEU* 1.3 76.0 - - + +
63C VAL* 1.3 63.9 + - + +
65C LEU* 3.4 7.9 + - - +
66C ARG* 3.0 61.4 + - + +
73C VAL* 4.5 7.4 - - + +
79C LEU* 3.7 25.1 - - + -
94C CYS* 5.7 1.1 - - - -
96C LEU* 3.8 27.8 - - + -
106C LEU* 4.2 11.9 - - + -
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Residues in contact with VAL 63 (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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59C SER* 3.3 16.0 + - - +
60C ARG* 3.7 9.4 - - - +
61C LEU 3.3 0.6 - - - -
62C ILE* 1.3 79.1 - - + +
64C GLU* 1.3 62.7 + - - +
66C ARG* 3.7 11.7 - - - +
67C ARG* 3.2 24.8 + - + +
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Residues in contact with GLU 64 (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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45C LEU* 3.7 30.0 - - + +
48C GLN* 6.1 0.2 - - - -
49C TYR* 3.3 27.9 + - + +
60C ARG 3.0 11.2 + - - +
61C LEU* 3.1 6.0 + - - +
63C VAL* 1.3 77.5 - - - +
65C LEU* 1.3 58.5 + - - +
67C ARG* 2.7 39.7 + - - +
68C LEU* 3.0 44.6 + - + +
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Residues in contact with LEU 65 (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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37C PHE* 3.9 18.2 - - + -
41C GLU* 5.8 0.7 - - + +
42C ILE* 3.8 21.8 - - + -
45C LEU* 3.6 24.9 - - + -
61C LEU* 2.8 40.3 + - + +
62C ILE* 3.8 5.2 - - - +
64C GLU* 1.3 72.9 - - - +
66C ARG* 1.3 53.7 - - - +
68C LEU* 3.6 3.2 - - + +
69C HIS* 2.7 43.2 + - + +
73C VAL* 4.0 16.1 - - + +
96C LEU* 4.1 25.1 - - + -
104C VAL* 4.5 13.5 - - + -
171C VAL* 5.9 0.4 - - + -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 3.0 41.5 + - - +
63C VAL* 3.7 11.2 - - - +
65C LEU* 1.3 76.4 - - - +
67C ARG* 1.3 58.3 + - - +
69C HIS 4.4 1.8 - - - -
70C PRO* 3.1 33.6 - - + +
73C VAL* 3.6 29.5 + - + +
74C LEU 2.5 35.2 + - - -
75C PRO* 3.6 5.8 - - - +
76C ASP* 2.0 37.4 + - - -
79C LEU* 4.5 3.0 - - - +
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Residues in contact with ARG 67 (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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63C VAL* 3.2 18.9 + - + +
64C GLU* 2.7 46.0 + - - +
66C ARG* 1.3 77.4 - - - +
68C LEU* 1.3 80.3 + - - +
70C PRO* 3.8 8.1 - - - +
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Residues in contact with LEU 68 (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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41C GLU* 4.5 12.6 - - + +
45C LEU* 3.7 34.5 - - + -
64C GLU* 3.0 29.7 + - - +
65C LEU* 3.8 1.6 - - - +
67C ARG* 1.3 103.0 - - - +
69C HIS* 1.3 82.8 + - + +
70C PRO* 3.6 5.0 - - - +
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Residues in contact with HIS 69 (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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36C VAL* 3.2 35.5 + - + +
37C PHE* 3.4 24.5 - + + -
41C GLU* 2.6 31.2 + - - -
65C LEU* 2.7 22.4 + - + +
66C ARG* 3.4 4.1 - - - +
68C LEU* 1.3 96.1 + - + +
70C PRO* 1.3 66.9 - - - +
71C GLY 3.5 0.2 + - - -
72C HIS* 3.3 32.4 + - + +
73C VAL* 3.9 7.9 - - + +
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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