Contacts of the helix formed by residues 129 - 140 (chain C) in PDB entry 1EFA
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 ASP 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C LEU* 1.3 75.1 - - - +
130C ASP* 1.3 61.0 + - - +
131C GLN 3.4 2.7 - - - +
132C ASP* 3.2 22.9 + - - +
133C ALA* 2.8 26.0 + - - +
192C VAL* 4.4 1.0 - - - +
195C ARG* 2.8 35.9 + - - +
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Residues in contact with ASP 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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128C LEU 4.9 0.7 - - - +
129C ASP* 1.3 73.4 - - - +
131C GLN* 1.3 64.0 + - + +
133C ALA* 3.3 2.1 + - - +
134C ILE* 2.9 36.2 + - + +
151C SER* 4.2 10.4 + - - -
153C GLN* 4.1 19.6 + - - +
154C THR* 2.8 36.4 + - + +
155C PRO* 4.7 5.8 - - + +
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Residues in contact with GLN 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 ASP* 3.4 2.2 - - + +
130C ASP* 1.3 77.3 - - + +
132C ASP* 1.3 62.4 + - - +
134C ILE* 3.2 13.1 + - + +
135C ALA* 2.8 29.3 + - - +
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Residues in contact with ASP 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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104C VAL* 2.9 45.3 - - + +
128C LEU* 4.2 8.2 - - + +
129C ASP* 3.2 29.3 + - - +
131C GLN* 1.3 74.8 - - - +
133C ALA* 1.3 67.5 - - - +
135C ALA* 3.1 9.1 + - - +
136C VAL* 2.8 27.2 + - - +
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Residues in contact with ALA 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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128C LEU* 3.9 16.5 - - + +
129C ASP 2.8 17.1 + - - +
130C ASP 3.5 4.7 - - - +
132C ASP* 1.3 76.2 - - - +
134C ILE* 1.3 53.0 + - - +
136C VAL* 3.2 1.7 + - - +
137C GLU* 2.8 36.8 + - - +
147C PHE* 3.6 5.0 - - + -
150C VAL* 3.9 17.0 - - + -
154C THR* 4.0 4.0 - - + -
156C ILE* 3.5 26.7 - - + -
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Residues in contact with ILE 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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130C ASP* 2.9 26.8 + - + +
131C GLN* 3.5 12.8 - - + +
132C ASP 3.2 0.2 - - - -
133C ALA* 1.3 75.0 - - - +
135C ALA* 1.3 62.7 + - - +
137C GLU* 3.4 11.0 + - + +
138C ALA* 2.9 23.7 + - + +
154C THR* 4.8 0.7 - - + -
155C PRO* 3.4 37.9 - - + +
156C ILE* 4.5 11.0 - - + -
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Residues in contact with ALA 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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108C LYS* 4.1 25.8 - - - +
131C GLN 2.8 13.6 + - - +
132C ASP* 3.1 12.8 + - - +
134C ILE* 1.3 77.8 - - - +
136C VAL* 1.3 62.9 + - - +
138C ALA* 2.9 18.2 + - - +
139C ALA* 2.9 13.7 + - - +
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Residues in contact with VAL 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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104C VAL* 4.6 6.7 - - + -
107C CYS* 4.3 12.1 - - - -
108C LYS* 4.3 22.0 - - + +
111C VAL* 3.8 26.9 - - + -
124C ILE* 4.2 8.5 - - + -
128C LEU* 4.1 15.5 - - + -
132C ASP 2.8 19.7 + - - +
133C ALA 3.5 7.4 - - - +
135C ALA* 1.3 72.0 - - - +
137C GLU* 1.3 66.9 + - - +
139C ALA* 2.9 19.1 + - - +
140C CYS* 3.2 14.1 + - - -
147C PHE* 4.0 19.1 - - + -
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Residues in contact with GLU 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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133C ALA 2.8 20.8 + - - +
134C ILE* 3.5 9.0 - - + +
136C VAL* 1.3 74.5 - - - +
138C ALA* 1.3 64.2 + - + +
140C CYS* 3.4 21.7 + - - +
143C VAL 5.1 2.9 - - - +
144C PRO* 5.9 0.3 - - - +
145C ALA* 4.1 22.0 + - - +
147C PHE* 3.9 16.6 - - + -
156C ILE* 4.0 25.6 - - + +
157C ASN* 4.7 7.4 + - - -
314C LYS* 5.7 1.0 + - - -
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Residues in contact with ALA 138 (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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134C ILE* 2.9 15.7 + - + +
135C ALA* 2.9 15.3 + - - +
137C GLU* 1.3 78.2 - - + +
139C ALA* 1.3 61.9 + - - +
140C CYS 3.2 5.2 + - - -
141C THR* 4.2 2.6 + - - -
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Residues in contact with ALA 139 (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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108C LYS* 5.8 10.1 - - + -
111C VAL* 4.8 11.2 - - + -
115C LEU* 3.3 12.2 - - + +
135C ALA 2.9 9.8 + - - +
136C VAL* 2.9 14.6 + - - +
138C ALA* 1.3 76.2 - - - +
140C CYS* 1.3 51.6 + - - +
141C THR* 2.6 27.0 + - - -
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Residues in contact with CYS 140 (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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111C VAL* 3.9 6.7 - - - -
115C LEU* 4.1 7.2 - - - -
122C LEU* 3.6 31.0 - - - -
124C ILE* 5.3 0.2 - - - -
136C VAL* 3.4 19.5 - - - -
137C GLU* 3.4 12.7 - - - +
138C ALA 3.1 5.7 - - - +
139C ALA* 1.3 71.8 - - - +
141C THR* 1.3 65.4 + - - +
142C ASN* 2.8 5.5 + - - -
143C VAL* 3.1 34.4 + - + +
145C ALA* 4.0 20.0 - - + -
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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