Contacts of the helix formed by residues 130 - 137 (chain C) in PDB entry 5ANC
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 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C MET* 1.3 75.4 - - - +
131C PRO* 1.4 67.7 - - + +
132C THR* 4.1 9.6 - - - +
133C GLN* 3.5 22.6 + - + +
134C THR* 2.6 37.3 + - - -
149C GLY 4.0 3.1 - - - +
150C GLN* 5.5 2.9 - - - +
167K LYS* 3.0 31.5 + - - -
171K GLU* 5.7 0.7 - - - +
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Residues in contact with PRO 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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129C MET 3.8 2.4 - - - +
130C GLU* 1.4 95.0 - - + +
132C THR* 1.3 63.5 + - - +
134C THR* 3.2 4.6 + - - +
135C SER* 2.9 28.6 + - - -
144C THR* 4.0 3.3 + - - -
146C ILE* 4.2 11.5 - - + -
147C ASN 3.8 25.8 - - - +
148C ARG 3.8 18.6 - - - +
149C GLY 3.7 13.5 - - - +
150C GLN* 4.6 3.1 - - - -
151C ILE* 3.7 21.8 - - + -
167K LYS* 4.6 1.6 - - - +
192K ARG* 4.6 12.3 - - - +
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Residues in contact with THR 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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130C GLU* 4.1 10.7 - - - +
131C PRO* 1.3 80.2 - - - +
133C GLN* 1.3 62.4 + - - +
135C SER* 3.2 7.5 + - - -
136C PHE* 2.9 58.6 + - + -
146C ILE* 4.6 23.1 - - + -
160K GLN* 5.2 10.1 - - + +
161K GLU* 6.0 1.3 - - - +
164K SER* 5.0 7.0 - - - +
192K ARG* 4.4 20.5 + - - +
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Residues in contact with GLN 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* 3.4 35.9 - - + +
130C GLU* 3.4 34.8 + - + +
131C PRO 3.2 0.4 - - - -
132C THR* 1.3 80.7 + - - +
134C THR* 1.3 59.2 - - - +
136C PHE* 3.2 14.2 + - + +
137C LEU* 2.9 39.7 + - + +
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Residues in contact with THR 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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129C MET* 4.3 3.5 + - - +
130C GLU 2.6 22.1 + - - -
131C PRO* 3.2 9.6 + - - +
133C GLN* 1.3 75.1 - - - +
135C SER* 1.3 62.9 + - - +
137C LEU* 3.2 29.5 + - - +
140C LEU* 4.8 4.9 - - + -
142C ILE 4.9 0.4 - - - +
143C ALA* 4.2 11.1 - - - +
144C THR* 3.2 31.2 - - + +
151C ILE* 4.4 4.6 + - + +
152C ASP 4.9 0.7 - - - +
153C ILE* 3.6 40.8 - - + +
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Residues in contact with SER 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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131C PRO 2.9 13.6 + - - -
132C THR* 3.4 9.0 - - - -
134C THR* 1.3 78.6 - - - +
136C PHE* 1.3 69.1 + - - +
137C LEU 4.1 0.3 - - - -
138C GLN* 3.0 25.3 + - - +
143C ALA* 5.3 0.2 - - - +
144C THR 3.5 24.5 + - - -
145C LYS* 4.2 7.3 - - - +
146C ILE* 4.2 19.2 - - - +
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Residues in contact with PHE 136 (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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132C THR* 2.9 53.2 + - + -
133C GLN* 3.4 12.1 - - + +
135C SER* 1.3 83.0 - - - +
137C LEU* 1.3 54.5 + - + +
138C GLN* 2.8 22.7 + - - +
146C ILE* 6.2 2.7 - - + -
161K GLU* 5.7 5.2 - - - -
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Residues in contact with LEU 137 (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* 3.7 29.6 - - + -
133C GLN* 2.9 27.7 + - + +
134C THR* 3.2 16.0 + - - +
135C SER 4.1 0.9 - - - -
136C PHE* 1.3 72.6 - - + +
138C GLN* 1.3 62.1 + - - +
139C ASP* 3.3 19.7 + - - +
140C LEU* 3.7 39.7 + - + +
143C ALA* 4.0 5.7 - - - +
176C LYS* 4.5 26.0 - - + +
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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