Contacts of the helix formed by residues 125 - 135 (chain c) in PDB entry 5JPQ
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 PRO 125 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124c LEU* 1.4 75.4 - - + -
126c ASP* 1.3 57.6 + - - +
127c LEU 3.2 1.6 - - - -
128c VAL* 3.3 14.4 + - + +
129c MET* 2.9 29.0 + - - +
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Residues in contact with ASP 126 (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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16062 C 4.6 10.5 - - - +
121c ASN* 4.2 13.7 - - + +
123c ILE 3.1 22.7 - - - +
124c LEU* 2.5 14.4 + - + +
125c PRO* 1.3 70.2 - - - +
127c LEU* 1.3 55.2 + - - +
129c MET* 3.2 8.8 + - - +
130c SER* 3.0 29.5 + - - -
126x PRO* 6.1 3.8 - - + -
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Residues in contact with LEU 127 (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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121c ASN 4.8 8.2 + - - +
122c LEU* 5.4 4.9 - - - +
124c LEU 2.8 15.0 + - - +
126c ASP* 1.3 73.8 - - - +
128c VAL* 1.3 58.1 + - - +
130c SER* 3.6 5.4 + - - -
131c ALA* 3.1 27.9 + - - +
155c SER* 5.9 7.9 - - - -
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Residues in contact with VAL 128 (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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124c LEU 4.4 0.2 + - - -
125c PRO* 3.3 16.2 + - + +
127c LEU* 1.3 78.6 - - - +
129c MET* 1.3 61.9 + - - +
131c ALA* 3.5 7.3 + - - +
132c GLN* 3.2 23.0 + - - +
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Residues in contact with MET 129 (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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125c PRO 2.9 13.6 + - - +
126c ASP* 3.3 13.9 - - - +
128c VAL* 1.3 76.5 - - - +
130c SER* 1.3 62.5 + - - +
132c GLN* 3.3 5.4 + - - +
133c ARG* 3.1 26.4 + - - +
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Residues in contact with SER 130 (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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89c LEU* 6.2 4.7 - - - -
126c ASP 3.0 16.3 + - - -
127c LEU* 4.0 6.5 - - - -
129c MET* 1.3 76.8 - - - +
131c ALA* 1.3 62.5 + - - +
133c ARG* 4.7 3.8 - - - +
134c GLU* 3.1 32.6 + - - +
136c LEU* 5.2 1.2 - - - +
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Residues in contact with ALA 131 (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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127c LEU 3.1 19.1 + - - +
128c VAL* 3.6 9.9 - - - +
130c SER* 1.3 77.3 - - - +
132c GLN* 1.3 56.9 + - - +
135c ARG* 3.0 22.9 + - - -
136c LEU* 3.1 31.7 + - - +
157c PHE* 5.2 11.9 - - + -
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Residues in contact with GLN 132 (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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128c VAL 3.2 13.6 + - - +
129c MET* 3.3 4.5 + - - +
131c ALA* 1.3 80.2 - - - +
133c ARG* 1.3 63.3 + - - +
134c GLU 3.4 0.5 + - - -
135c ARG* 3.5 11.3 + - - +
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Residues in contact with ARG 133 (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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129c MET 3.1 17.1 + - - +
130c SER* 4.5 3.4 - - - +
132c GLN* 1.3 77.1 - - - +
134c GLU* 1.3 58.7 + - + +
135c ARG 3.5 0.2 - - - -
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Residues in contact with GLU 134 (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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87c ARG* 5.8 0.5 - - - +
89c LEU* 5.6 5.6 - - + -
130c SER* 3.1 20.2 + - - +
133c ARG* 1.3 78.1 - - - +
135c ARG* 1.3 70.6 + - - +
136c LEU* 3.3 11.2 + - + +
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Residues in contact with ARG 135 (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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87c ARG* 3.9 14.2 - - - +
131c ALA 3.0 11.3 + - - -
132c GLN* 3.5 9.5 + - - +
133c ARG 3.5 0.2 - - - -
134c GLU* 1.3 81.2 - - - +
136c LEU* 1.3 57.2 + - - +
137c SER 4.2 1.1 + - - -
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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