Contacts of the helix formed by residues 114 - 120 (chain C) in PDB entry 1PR1
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 LYS 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP* 3.3 19.8 + - - -
123A HIS* 2.8 43.4 + - - +
124A ASP* 5.1 4.2 + - - +
112C ASP 4.0 0.8 + - - +
113C SER* 1.3 74.4 + - - +
115C VAL* 1.3 65.9 + - - +
116C ASN 3.3 2.2 - - - -
117C ARG* 3.1 26.4 + - + +
118C ILE* 3.0 35.1 + - + +
157C ASP* 5.0 0.8 + - - -
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 4.1 24.7 - - + -
67C PRO* 5.9 4.9 - - + -
70C SER* 5.4 1.6 - - - +
113C SER* 3.2 18.4 + - - +
114C LYS* 1.3 77.4 - - - +
116C ASN* 1.3 66.8 + - - +
118C ILE* 3.3 22.4 + - + +
119C ARG* 2.7 54.8 + - - +
184C GLY* 5.0 3.8 - - - -
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Residues in contact with ASN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR* 4.6 12.5 - - + +
113C SER* 5.0 2.6 + - - +
114C LYS 3.3 0.8 - - - -
115C VAL* 1.3 75.7 - - - +
117C ARG* 1.3 61.9 + - + +
118C ILE 3.1 1.3 - - - -
119C ARG* 2.8 38.8 + - - +
120C PHE* 2.7 33.2 + - - +
123C HIS 5.2 0.4 - - - -
125C PHE* 3.9 35.0 - - + +
127C ALA* 4.0 9.4 - - - +
183C ALA* 3.4 22.6 + - - +
187C GLY* 3.9 9.9 - - - -
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Residues in contact with ARG 117 (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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113C SER 4.9 5.8 + - - +
114C LYS* 3.1 29.6 + - + +
116C ASN* 1.3 79.1 - - + +
118C ILE* 1.3 62.2 + - + +
119C ARG 3.3 0.5 + - - -
121C LYS* 3.4 4.2 + - - -
122C ASP* 2.7 59.0 + - - +
123C HIS 3.9 16.4 + - - +
124C ASP* 4.8 14.6 + - - -
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Residues in contact with ILE 118 (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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123A HIS* 3.8 31.6 - - + +
114C LYS* 3.0 34.6 + - + +
115C VAL* 3.4 15.3 - - + +
116C ASN 3.1 0.2 - - - -
117C ARG* 1.3 79.6 - - + +
119C ARG* 1.3 59.3 - - + +
121C LYS* 4.6 2.6 + - - -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER* 4.7 5.7 + - - -
115C VAL* 2.7 43.7 + - - +
116C ASN* 2.8 34.7 + - - +
118C ILE* 1.3 81.8 - - + +
120C PHE* 1.3 63.9 + - + +
121C LYS* 3.5 6.0 + - - +
125C PHE* 6.2 3.4 - - + -
184C GLY 4.4 4.2 + - - -
187C GLY* 3.8 22.6 + - - -
188C VAL* 3.6 25.7 - - - +
191C GLU* 2.8 33.7 + - - +
192C PHE* 5.3 1.0 - - - -
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Residues in contact with PHE 120 (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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116C ASN 2.7 20.5 + - - +
117C ARG 3.5 0.2 + - - -
119C ARG* 1.3 77.7 - - + +
121C LYS* 1.3 69.7 + - - +
122C ASP 3.2 2.5 - - - -
123C HIS* 2.9 34.5 + + + +
124C ASP 3.8 15.9 - - - -
125C PHE* 3.6 50.7 - + + -
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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