Contacts of the helix formed by residues 135 - 148 (chain C) in PDB entry 1OFG
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 VAL 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C SER* 1.3 71.5 - - - +
136C ALA* 1.3 58.5 + - - +
138C CYS* 3.2 11.8 - - - +
139C GLN* 3.1 26.6 + - + +
350C MET* 4.3 15.4 - - + +
353C VAL* 4.3 1.3 - - + -
354C ARG* 3.9 49.8 - - + +
357C GLN* 4.1 20.9 - - + -
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Residues in contact with ALA 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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134C SER* 3.3 7.4 + - - +
135C VAL* 1.3 75.5 - - - +
137C ASP* 1.3 62.3 + - - +
139C GLN* 3.3 8.7 + - - +
140C ARG* 2.9 33.7 + - + +
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Residues in contact with ASP 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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109C SER 5.4 3.1 - - - +
112C ALA* 4.0 18.2 - - + +
132C ALA* 3.7 14.1 - - + +
133C THR* 4.6 8.1 + - - -
134C SER* 3.0 27.5 + - - +
136C ALA* 1.3 75.3 - - - +
138C CYS* 1.3 59.4 + - - +
140C ARG* 3.4 21.2 + - - +
141C MET* 3.1 34.6 + - - +
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Residues in contact with CYS 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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131C MET* 3.3 44.9 - - - +
132C ALA* 3.9 7.0 - - - -
134C SER 3.4 19.7 + - - -
135C VAL* 3.2 10.5 + - - +
137C ASP* 1.3 76.7 - - - +
139C GLN* 1.3 63.0 + - - +
141C MET* 3.4 3.5 - - - +
142C ILE* 3.2 29.8 + - - +
350C MET* 3.5 20.4 - - + -
353C VAL* 3.9 22.2 - - - -
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Residues in contact with GLN 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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135C VAL* 3.1 10.4 + - + +
136C ALA* 3.3 13.7 - - - +
138C CYS* 1.3 79.5 - - - +
140C ARG* 1.3 55.9 + - - +
142C ILE* 3.3 16.0 + - - +
143C ASP* 3.0 51.1 + - - +
350C MET* 3.5 24.2 - - - +
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Residues in contact with ARG 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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112C ALA* 6.2 0.2 - - - -
116C ILE* 4.0 20.2 - - + +
136C ALA* 2.9 17.3 + - + +
137C ASP* 3.4 28.3 - - - +
139C GLN* 1.3 74.8 - - - +
141C MET* 1.3 59.6 + - - +
143C ASP* 3.5 8.6 + - - +
144C ALA* 3.0 29.5 + - - +
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Residues in contact with MET 141 (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 HIS 4.4 1.3 - - - +
112C ALA* 3.7 35.4 - - + +
115C ALA* 3.9 19.7 - - + -
116C ILE* 4.3 7.2 - - + -
119C PHE* 3.6 10.3 - - - -
127C CYS* 3.9 23.6 - - + -
131C MET* 3.7 47.8 - - + +
132C ALA* 4.2 6.5 - - - -
137C ASP 3.1 15.2 + - - +
138C CYS 3.4 8.1 - - - +
140C ARG* 1.3 76.9 - - - +
142C ILE* 1.3 59.5 + - - +
144C ALA* 3.6 0.9 + - - +
145C ALA* 3.1 26.7 + - - +
152C LEU* 4.2 10.5 - - + +
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Residues in contact with ILE 142 (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 MET* 4.0 8.7 - - + -
138C CYS 3.2 13.6 + - - +
139C GLN* 3.3 20.4 + - - +
141C MET* 1.3 73.6 - - - +
143C ASP* 1.3 61.1 + - - +
145C ALA* 3.3 7.3 + - - +
146C LYS* 3.0 42.1 + - + +
152C LEU* 4.3 3.8 - - + -
346C GLY* 3.5 28.9 - - - +
347C GLU* 3.7 22.7 - - + +
350C MET* 3.5 33.4 - - + -
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Residues in contact with ASP 143 (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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139C GLN* 3.0 43.6 + - - +
140C ARG* 3.5 10.2 - - - +
142C ILE* 1.3 77.6 - - - +
144C ALA* 1.3 55.3 + - - +
146C LYS* 3.3 13.9 + - - +
147C ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 144 (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 ILE* 3.8 26.0 - - + +
119C PHE* 3.5 16.5 - - + +
120C LYS* 6.3 0.7 - - + -
140C ARG 3.0 18.5 + - - +
141C MET 3.7 6.5 - - - +
142C ILE 3.3 0.2 - - - -
143C ASP* 1.3 73.5 - - - +
145C ALA* 1.3 60.3 + - - +
147C ALA* 3.9 7.2 - - - +
148C ALA* 3.1 27.9 + - - +
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Residues in contact with ALA 145 (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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119C PHE* 3.4 30.7 - - + -
141C MET 3.1 13.7 + - - +
142C ILE* 3.4 10.8 - - - +
144C ALA* 1.3 76.5 - - - +
146C LYS* 1.3 60.0 + - - +
148C ALA 3.4 0.9 + - - -
149C ASN* 3.0 7.4 + - - -
150C LYS 2.9 39.9 + - - +
152C LEU* 4.2 11.9 - - + +
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Residues in contact with LYS 146 (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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142C ILE* 3.0 30.0 + - + +
143C ASP* 3.4 14.1 - - - +
145C ALA* 1.3 80.7 - - + +
147C ALA* 1.3 61.6 + - - +
149C ASN* 3.4 18.9 + - - +
150C LYS 5.2 0.2 - - - -
347C GLU* 5.6 2.9 - - - +
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Residues in contact with ALA 147 (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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143C ASP 3.0 17.5 + - - +
144C ALA* 3.9 8.7 - - - +
146C LYS* 1.3 78.5 - - - +
148C ALA* 1.3 58.0 + - - +
149C ASN* 3.6 1.4 + - - +
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Residues in contact with ALA 148 (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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119C PHE* 3.3 30.3 - - + +
122C GLY* 5.5 1.2 - - - -
144C ALA 3.1 19.2 + - - +
145C ALA 3.9 3.4 - - - +
146C LYS 3.3 0.2 - - - -
147C ALA* 1.3 77.5 - - - +
149C ASN* 1.3 69.5 - - - +
150C LYS* 3.6 23.0 + - + +
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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