Contacts of the helix formed by residues 54 - 63 (chain C) in PDB entry 3HSR
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 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C LEU* 1.3 80.9 - - - +
55C ILE* 1.3 64.0 + - - +
56C LYS* 3.1 12.8 + - - +
57C LYS* 2.9 30.3 + - - +
58C LEU* 3.0 17.8 + - - +
94C LEU 4.7 8.7 - - - +
95C GLN* 3.2 19.6 + - - +
96C ILE* 4.1 1.6 - - - -
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Residues in contact with ILE 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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54C ASN* 1.3 75.3 - - - +
56C LYS* 1.3 58.2 + - + +
58C LEU* 3.6 2.0 + - + -
59C GLY* 2.9 22.9 + - - -
66C SER* 4.7 11.9 - - - +
69C LEU* 3.5 23.5 - - + +
70C THR* 5.0 9.6 - - - +
73C LEU* 2.4 36.6 - - + -
84C ARG* 3.8 15.9 - - - +
94C LEU 5.2 5.1 + - - +
96C ILE* 2.3 44.2 - - + -
144C GOL 4.7 1.4 + - - -
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Residues in contact with LYS 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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54C ASN* 3.1 9.8 + - - +
55C ILE* 1.3 76.7 - - + +
57C LYS* 1.3 61.9 + - - +
59C GLY 3.3 0.5 + - - -
60C GLU* 3.0 26.0 + - - +
66C SER* 2.8 32.4 + - - +
144C GOL 3.2 35.0 + - - +
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Residues in contact with LYS 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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51C GLU* 4.6 2.4 + - - -
53C LEU* 3.1 25.3 - - + +
54C ASN* 2.9 22.9 + - - +
56C LYS* 1.3 72.9 - - - +
58C LEU* 1.3 60.2 + - - +
60C GLU* 3.3 8.4 + - + +
61C ARG* 2.9 53.1 + - + +
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Residues in contact with LEU 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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43C VAL* 3.8 26.0 - - + -
46C ALA* 4.2 20.2 - - + +
47C ILE* 3.9 22.2 - - + -
53C LEU* 3.4 27.3 - - + +
54C ASN 3.0 14.0 + - - +
55C ILE* 3.8 5.2 - - - +
57C LYS* 1.3 75.8 - - - +
59C GLY* 1.3 62.9 + - - +
61C ARG* 3.1 6.9 + - + +
62C VAL* 3.1 31.0 + - + +
69C LEU* 3.8 21.5 - - + -
73C LEU* 4.1 5.6 - - + -
96C ILE* 4.0 20.0 - - + -
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Residues in contact with GLY 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 ILE 2.9 12.9 + - - -
56C LYS 3.7 0.4 - - - -
57C LYS 3.3 0.2 - - - -
58C LEU* 1.3 73.6 - - - +
60C GLU* 1.3 58.1 + - - +
62C VAL* 4.5 0.9 - - - -
63C PHE* 2.8 26.7 + - - -
64C LEU 3.0 28.4 + - - +
69C LEU* 3.5 15.0 - - - +
144C GOL 3.5 12.1 - - - -
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Residues in contact with GLU 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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56C LYS 3.0 13.5 + - - +
57C LYS* 3.7 10.2 - - - +
59C GLY* 1.3 77.4 - - - +
61C ARG* 1.3 63.0 + - - +
62C VAL 3.5 0.3 + - - -
63C PHE* 3.6 21.0 + - - +
142C PHE 5.7 0.5 - - - +
144C GOL 4.0 11.6 + - - +
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Residues in contact with ARG 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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46C ALA* 2.7 48.8 + - + +
47C ILE* 4.3 0.2 - - - +
48C GLU* 4.4 4.9 - - - +
51C GLU* 2.7 39.4 + - - -
53C LEU* 3.8 12.8 - - - +
57C LYS* 2.9 44.1 + - + +
58C LEU* 3.1 8.7 + - + +
60C GLU* 1.3 80.4 - - - +
62C VAL* 1.3 58.0 + - + +
63C PHE* 3.6 12.3 - - - -
14D PHE* 3.6 17.1 - - + -
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Residues in contact with VAL 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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42C ILE* 3.9 25.1 - - + +
43C VAL* 4.7 7.6 - - + -
46C ALA* 3.2 35.2 - - + -
58C LEU* 3.1 25.1 + - + +
59C GLY* 4.2 0.4 - - - +
61C ARG* 1.3 78.2 - - - +
63C PHE* 1.3 61.9 + - - +
64C LEU* 3.3 27.9 + - + -
69C LEU* 5.0 1.3 - - + -
14D PHE* 4.8 7.0 - - + -
17D TYR* 2.8 13.7 + - - -
21D LYS* 2.6 29.1 + - - -
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Residues in contact with PHE 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 GLY 2.8 11.0 + - - -
60C GLU* 3.6 13.1 + - - +
61C ARG* 3.5 15.9 - - - -
62C VAL* 1.3 83.8 - - - +
64C LEU* 1.3 55.9 + - - +
138C VAL* 5.2 4.7 - - + -
142C PHE* 3.9 32.8 - + + -
14D PHE* 4.5 4.7 - + - -
17D TYR* 4.9 0.2 - - + -
18D VAL* 3.7 43.7 - - + -
21D LYS* 2.6 36.1 + - - +
22D GLU* 3.8 20.9 - - + +
25D LYS* 3.5 13.5 + - - -
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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