Contacts of the helix formed by residues 77 - 84 (chain C) in PDB entry 5HP1
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 PHE 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C THR* 3.1 36.8 - - + -
75C VAL* 3.3 30.3 + - + -
76C ASP* 1.3 72.5 + - - +
78C ARG* 1.3 54.9 + - - +
79C GLU 3.0 3.8 + - - -
80C LEU* 3.0 28.7 + - + +
81C ASN* 2.6 42.5 + - - +
128C THR* 3.6 33.0 - - + -
146C TYR* 4.6 2.0 - + - -
150C PRO* 3.5 28.7 - - + -
151C GLN 4.0 0.7 - - - -
152C GLY 3.2 19.6 + - - +
153C TRP* 3.6 22.9 - - + -
0E A 4.8 2.6 - - - -
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Residues in contact with ARG 78 (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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24C TRP* 4.9 0.8 - - - -
76C ASP* 2.8 36.0 + - - +
77C PHE* 1.3 77.3 - - - +
79C GLU* 1.3 57.2 + - - +
81C ASN* 3.4 10.6 - - - +
82C LYS* 2.9 43.1 + - - +
-1E T 3.3 40.0 + - - +
0E A 3.2 37.9 + - - +
1E C 3.4 12.6 - - - +
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Residues in contact with GLU 79 (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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19C PRO* 4.2 11.0 - - + -
20C LYS 5.0 0.9 - - - +
21C VAL* 3.9 30.6 - - + +
58C THR* 6.2 0.2 - - + -
76C ASP* 5.1 2.1 + - - +
77C PHE 3.0 1.2 + - - -
78C ARG* 1.3 74.9 - - - +
80C LEU* 1.3 66.1 + - - +
82C LYS* 3.1 27.8 + - - +
83C ARG* 2.7 68.0 + - - +
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Residues in contact with LEU 80 (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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12C LEU* 4.1 8.7 - - + -
19C PRO* 3.8 33.4 - - + +
58C THR* 5.6 0.2 - - - +
77C PHE* 3.0 39.1 + - + +
79C GLU* 1.3 77.6 - - - +
81C ASN* 1.3 50.3 + - - +
83C ARG* 3.0 3.9 + - + +
84C THR* 2.3 45.6 + - - +
124C PHE* 3.5 37.0 - - + -
127C TYR* 3.8 20.0 - - + +
128C THR* 4.3 5.6 - - + -
153C TRP* 4.0 13.5 - - + +
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Residues in contact with ASN 81 (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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77C PHE 2.6 29.7 + - - +
78C ARG* 3.4 12.0 - - - +
79C GLU 3.1 0.2 - - - -
80C LEU* 1.3 73.6 - - - +
82C LYS* 1.3 61.6 + - - +
84C THR* 3.3 5.9 + - - -
152C GLY 3.3 8.5 + - - -
153C TRP* 3.2 14.6 - - - -
154C LYS* 2.8 66.2 + - + +
1E C 3.2 34.4 + - - -
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Residues in contact with LYS 82 (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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13C LYS* 3.3 28.0 + - - +
16C MET* 4.4 3.4 - - - +
78C ARG* 2.9 28.4 + - - +
79C GLU* 3.1 30.6 + - - +
81C ASN* 1.3 75.9 - - + +
83C ARG* 1.3 62.9 + - + +
154C LYS* 5.0 0.4 - - - +
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Residues in contact with ARG 83 (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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12C LEU* 3.4 14.9 - - + +
13C LYS* 2.8 29.7 + - - +
16C MET* 4.2 24.1 - - + +
17C ASP* 2.9 42.9 + - - +
18C GLY* 3.5 18.4 + - - -
19C PRO* 4.5 1.1 - - - -
20C LYS 5.8 0.7 - - - -
79C GLU* 2.7 56.7 + - - +
80C LEU* 3.0 8.5 + - + +
82C LYS* 1.3 77.4 - - + +
84C THR* 1.3 58.9 + - - +
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Residues in contact with THR 84 (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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10C VAL* 4.0 5.4 - - + -
11C LYS 4.0 3.6 - - - +
12C LEU* 4.0 4.7 - - - -
13C LYS* 3.3 13.5 - - - -
80C LEU* 2.3 38.1 + - - +
81C ASN* 3.3 6.2 + - - -
83C ARG* 1.3 78.6 - - - +
85C GLN* 1.3 76.2 + - + +
87C PHE* 4.4 2.5 - - + -
124C PHE* 3.6 23.1 - - + -
153C TRP* 3.4 32.3 + - + +
154C LYS* 2.9 19.5 + - - -
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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