Contacts of the helix formed by residues 56 - 72 (chain C) in PDB entry 1HYH
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 GLU 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C ALA 3.3 7.3 + - - +
55C ASN* 1.3 71.4 + - - +
57C ALA* 1.3 55.9 + - - +
59C VAL* 3.5 5.2 - - - +
60C LYS* 3.0 37.5 + - + +
81C ILE* 3.7 19.6 - - - +
82C ASN* 2.7 32.2 + - - +
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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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244A GLY* 3.9 21.3 - - - +
55C ASN* 3.0 10.3 + - - +
56C GLU* 1.3 77.4 - - - +
58C LYS* 1.3 57.2 + - - +
60C LYS* 3.7 4.3 - - - +
61C ALA* 2.9 30.3 + - - +
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Residues in contact with LYS 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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244A GLY 3.7 10.4 + - - +
245A LYS* 3.6 26.0 - - + -
247A TYR* 4.3 13.0 + - - -
29C LEU* 2.9 27.2 + - + +
30C GLY* 4.5 6.2 + - - -
34C ALA* 4.2 9.9 - - - +
53C ASP* 4.8 2.7 - - - +
55C ASN* 3.3 28.5 + - + +
57C ALA* 1.3 76.8 - - - +
59C VAL* 1.3 64.3 + - - +
61C ALA* 3.1 5.2 + - - +
62C ASP* 2.5 54.8 + - - +
330C NAD 4.8 9.2 - - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 4.1 9.2 - - + -
51C PHE* 3.6 36.5 - - + +
53C ASP* 3.7 25.8 - - + +
55C ASN 3.3 7.8 + - - +
56C GLU 3.5 10.5 - - - +
58C LYS* 1.3 78.8 - - - +
60C LYS* 1.3 61.2 + - - +
62C ASP* 3.4 6.9 + - - +
63C GLN* 3.0 28.4 + - - +
81C ILE* 3.9 17.4 - - + +
82C ASN* 3.7 26.2 - - - +
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Residues in contact with LYS 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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240A THR* 5.6 5.2 - - + -
56C GLU* 3.0 24.4 + - + +
57C ALA* 3.8 4.7 - - - +
59C VAL* 1.3 77.5 - - - +
61C ALA* 1.3 60.5 + - - +
63C GLN* 3.0 27.9 + - - +
64C ILE* 3.1 47.5 + - + +
67C GLN* 5.6 1.2 - - - +
81C ILE* 3.9 19.2 - - + +
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Residues in contact with ALA 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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240A THR* 4.6 2.9 - - - +
241A VAL* 3.8 38.1 - - - +
244A GLY* 3.9 11.2 - - - -
245A LYS* 4.0 14.1 - - + +
57C ALA 2.9 17.3 + - - +
58C LYS 3.1 5.1 + - - +
60C LYS* 1.3 75.0 - - - +
62C ASP* 1.3 60.1 + - - +
64C ILE* 3.5 2.2 + - - -
65C ASP* 3.0 29.7 + - - +
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Residues in contact with ASP 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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245A LYS* 2.8 33.4 + - - +
247A TYR* 5.0 0.5 + - - -
250A TYR* 3.8 11.4 + - - -
29C LEU* 3.8 14.8 - - + +
34C ALA* 4.0 7.0 - - - +
51C PHE* 4.8 7.2 - - + -
58C LYS* 2.5 41.9 + - - +
59C VAL* 3.7 9.0 - - - +
61C ALA* 1.3 73.7 - - - +
63C GLN* 1.3 65.5 + - - +
65C ASP* 3.2 1.4 + - - +
66C PHE* 2.9 41.3 + - + -
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Residues in contact with GLN 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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51C PHE* 4.7 3.1 - - - -
59C VAL 3.0 16.9 + - - +
60C LYS* 3.0 39.5 + - - +
61C ALA 3.3 0.2 - - - -
62C ASP* 1.3 76.0 - - - +
64C ILE* 1.3 55.4 + - - +
66C PHE* 3.3 4.4 + - - +
67C GLN* 2.9 55.4 + - - +
79C ILE* 3.0 45.6 + - + +
80C VAL* 4.3 2.8 - - - +
81C ILE* 4.0 24.4 - - + +
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Residues in contact with ILE 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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177A ARG* 4.1 27.6 - - - +
233A GLU* 5.3 8.7 - - - +
237A GLY* 4.4 5.2 - - - +
240A THR* 4.0 27.4 - - + -
241A VAL* 3.5 20.2 - - + -
60C LYS* 3.1 40.5 + - + +
61C ALA* 3.9 3.1 - - - +
63C GLN* 1.3 78.4 - - - +
65C ASP* 1.3 57.3 + - - +
67C GLN* 3.1 19.9 + - - +
68C ASP* 2.9 32.5 + - - +
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Residues in contact with ASP 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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174A ARG* 5.1 2.1 + - - -
241A VAL* 4.0 13.4 - - + +
245A LYS* 2.7 28.4 + - - +
248A THR* 4.3 5.9 - - - -
249A SER 2.9 22.5 + - - -
250A TYR* 3.2 15.4 + - + +
251A GLY* 3.0 28.2 + - - -
61C ALA 3.0 18.2 + - - +
62C ASP 3.2 4.7 + - - +
64C ILE* 1.3 77.4 - - - +
66C PHE* 1.3 59.1 + - - +
68C ASP* 3.3 18.8 + - - +
69C ALA 3.4 8.1 + - - -
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Residues in contact with PHE 66 (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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250A TYR* 3.5 51.1 - + + -
29C LEU* 5.4 0.7 - - + -
34C ALA* 4.1 1.8 - - - -
37C ALA* 3.8 11.0 - - + -
38C HIS* 3.7 33.0 - + + -
41C ILE* 3.5 27.8 - - + -
51C PHE* 3.7 30.7 - + - -
62C ASP* 2.9 30.2 + - + +
63C GLN 3.7 0.2 - - - +
65C ASP* 1.3 75.3 - - - +
67C GLN* 1.3 62.4 + - - +
69C ALA* 3.2 17.1 + - + +
70C MET* 3.3 19.0 + - + +
79C ILE* 3.4 19.5 - - + -
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Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA 4.9 0.5 - - - +
177A ARG* 3.5 27.0 - - + +
181A GLU* 3.7 21.3 + - - +
187A PRO* 4.9 3.1 - - - +
60C LYS* 5.6 1.0 - - - +
63C GLN* 2.9 45.5 + - + +
64C ILE* 3.1 23.9 + - - +
66C PHE* 1.3 75.3 - - - +
68C ASP* 1.3 60.5 + - - +
70C MET* 3.4 25.0 + - + +
71C ALA 4.5 1.7 + - - -
79C ILE* 4.2 15.6 + - + +
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Residues in contact with ASP 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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170A LEU* 4.6 3.3 - - + +
173A ALA* 3.2 31.9 - - - +
174A ARG* 2.9 47.7 + - + +
177A ARG* 2.7 31.7 + - - -
237A GLY 5.3 0.5 - - - +
241A VAL* 4.8 2.4 - - - +
251A GLY* 4.1 14.3 - - - +
64C ILE* 2.9 22.6 + - - +
65C ASP* 3.4 14.1 - - - +
66C PHE 3.2 0.4 - - - -
67C GLN* 1.3 78.4 - - - +
69C ALA* 1.3 58.7 + - - +
70C MET 3.5 0.2 + - - -
71C ALA 4.0 2.8 + - - -
72C ASN* 4.7 1.6 + - - -
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Residues in contact with ALA 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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250A TYR* 3.6 14.4 - - + +
251A GLY* 4.1 6.5 - - - -
254A THR* 3.5 28.1 - - - +
65C ASP 3.4 7.1 + - - +
66C PHE* 3.3 17.5 - - + +
68C ASP* 1.3 77.1 - - - +
70C MET* 1.3 62.9 + - - +
72C ASN* 3.0 15.4 + - - -
73C LEU* 3.1 23.4 + - + +
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Residues in contact with MET 70 (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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186A ASP* 6.0 0.2 - - - +
187A PRO* 3.9 18.2 - - + -
188A ARG* 3.7 17.7 + - - +
41C ILE* 3.8 22.7 - - + -
66C PHE 3.3 17.0 + - - +
67C GLN* 3.5 18.8 - - + +
68C ASP 3.3 1.2 - - - -
69C ALA* 1.3 75.9 - - - +
71C ALA* 1.3 63.2 + - - +
72C ASN 3.2 1.0 + - - -
73C LEU* 3.3 35.6 + - + +
75C ALA 4.0 9.7 - - - +
76C HIS* 4.0 12.8 - - + +
77C GLY* 3.7 43.3 - - - +
79C ILE* 4.9 5.2 - - + -
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Residues in contact with ALA 71 (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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173A ALA* 3.9 22.7 - - + +
176A GLN* 3.3 41.7 + - + +
187A PRO* 4.4 9.8 - - + +
188A ARG* 3.8 21.6 - - - +
258A ARG* 3.9 8.8 + - - -
67C GLN 4.5 1.2 + - - -
68C ASP 4.0 1.6 + - - -
69C ALA 3.2 1.6 + - - -
70C MET* 1.3 79.0 - - - +
72C ASN* 1.3 61.8 + - - +
73C LEU 4.7 0.3 - - - +
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Residues in contact with ASN 72 (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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169A LEU* 3.8 17.0 + - - +
173A ALA* 3.8 20.0 - - - +
176A GLN* 5.1 1.9 - - - +
251A GLY 4.9 0.4 + - - -
254A THR* 3.4 28.5 - - + +
255A SER* 2.9 29.2 + - - -
258A ARG* 2.9 52.0 + - - +
68C ASP 4.7 2.0 + - - -
69C ALA 3.0 4.9 + - - +
71C ALA* 1.3 79.6 - - - +
73C LEU* 1.3 59.9 + - - +
74C GLU* 4.9 4.3 - - - +
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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