Contacts of the helix formed by residues 138 - 152 (chain C) in PDB entry 4OGB
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 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C LYS 3.2 11.2 - - - +
137C ILE* 1.3 90.6 - - + +
139C VAL* 1.3 64.2 + - - +
140C ASP* 3.4 17.9 - - - +
141C THR* 3.2 21.5 + - + +
142C LEU* 3.0 18.9 + - - +
248C ILE 5.5 0.9 - - - +
250C GLN* 4.0 29.2 - - + +
251C ASN* 4.5 2.9 - - - +
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Residues in contact with VAL 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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123C HIS* 3.9 29.4 - - + +
127C GLN* 5.8 1.3 - - - +
132C LEU* 4.2 15.0 - - + -
137C ILE 3.4 1.6 + - - +
138C PRO* 1.3 72.9 - - + +
140C ASP* 1.3 67.3 + - - +
142C LEU* 3.3 2.1 + - - +
143C ILE* 3.0 39.3 + - + +
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Residues in contact with ASP 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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138C PRO* 3.4 19.0 - - - +
139C VAL* 1.3 78.8 + - - +
141C THR* 1.3 60.1 + - - -
143C ILE* 3.9 7.3 - - - +
144C THR* 2.8 37.9 + - - +
245C ASN* 3.1 24.0 + - - +
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Residues in contact with THR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PRO* 3.2 30.3 + - + +
139C VAL 3.1 0.6 - - - -
140C ASP* 1.3 78.7 + - - +
142C LEU* 1.3 64.9 + - - +
145C TYR* 3.0 23.9 + - - +
245C ASN* 2.6 39.6 + - - +
247C ASP 3.6 36.3 - - - +
248C ILE* 4.1 4.3 - - - +
250C GLN* 3.7 10.1 + - - +
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Residues in contact with LEU 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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123C HIS* 3.4 29.8 - - + +
126C PHE* 3.9 36.6 - - + -
132C LEU* 3.7 24.0 - - + -
137C ILE* 3.8 9.6 - - + -
138C PRO 3.0 12.7 + - - +
139C VAL 3.3 6.5 + - - +
141C THR* 1.3 77.4 - - - +
143C ILE* 1.3 58.0 + - - +
145C TYR* 3.5 0.7 + - - +
146C LEU* 2.9 58.2 + - + +
248C ILE* 3.6 25.1 - - + +
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Residues in contact with ILE 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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349A GLU 4.9 4.7 - - - +
119C THR* 4.7 8.0 - - + +
123C HIS* 4.6 24.5 - - + +
139C VAL* 3.0 36.6 + - + +
140C ASP* 3.9 6.5 - - - +
142C LEU* 1.3 76.3 - - + +
144C THR* 1.3 57.5 + - - +
146C LEU* 4.0 6.1 - - + +
147C MET* 3.0 64.1 + - + +
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Residues in contact with THR 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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349A GLU 5.5 0.6 + - - -
350A ARG* 4.3 35.1 + - + +
140C ASP* 2.8 23.3 + - - +
143C ILE* 1.3 79.1 - - - +
145C TYR* 1.3 57.6 + - - +
147C MET* 3.5 7.2 + - - +
148C THR* 2.8 35.1 + - - +
244C GLU 3.7 14.1 - - - +
245C ASN* 3.4 20.0 + - + +
246C CYS* 3.6 18.4 - - - -
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Residues in contact with TYR 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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122C MET* 6.0 0.9 - - + -
141C THR 3.0 13.6 + - - +
144C THR* 1.3 74.7 - - - +
146C LEU* 1.3 67.8 + - + +
148C THR* 3.1 2.1 + - - -
149C LEU* 2.7 58.4 + - + +
195C PHE* 3.2 33.2 - + - -
199C ILE* 3.5 10.7 - - - +
237C GLY 2.8 27.8 + - - -
240C LEU* 3.8 20.9 - - + -
241C LEU* 3.7 19.5 - - + -
246C CYS* 3.3 36.3 - - - +
248C ILE* 3.6 20.4 - - + -
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.7 5.4 - - + +
119C THR* 3.5 38.7 + - + +
122C MET* 3.7 44.9 - - + -
123C HIS* 3.9 10.1 - - + +
142C LEU* 2.9 50.3 + - + +
143C ILE* 4.0 3.8 - - - +
145C TYR* 1.3 85.0 - - + +
147C MET* 1.3 57.9 + - - +
149C LEU* 3.3 9.3 + - + +
150C GLU* 2.8 33.3 + - - +
248C ILE* 6.1 0.2 - - + -
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Residues in contact with MET 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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349A GLU* 3.4 57.0 - - + +
350A ARG* 4.3 12.1 - - - +
116C ARG* 3.0 30.7 + - + +
119C THR* 3.7 16.2 - - + +
143C ILE* 3.0 46.7 + - + +
144C THR* 3.7 4.9 - - - +
146C LEU* 1.3 76.0 - - - +
148C THR* 1.3 57.2 + - - +
151C ASP* 2.9 31.1 + - - -
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Residues in contact with THR 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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350A ARG* 3.2 26.5 + - - +
144C THR 2.8 22.0 + - - -
145C TYR* 3.1 4.5 + - - -
147C MET* 1.3 73.2 - - - +
149C LEU* 1.3 64.7 + - - +
151C ASP* 3.1 9.4 + - - +
152C HIS* 3.0 23.3 - - + -
240C LEU* 4.0 24.5 - - + -
243C GLU* 3.5 24.2 - - - +
246C CYS* 3.6 16.0 - - - -
501C EDO 3.7 10.5 - - - +
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Residues in contact with LEU 149 (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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118C LEU* 4.0 13.0 - - + -
145C TYR* 2.7 44.4 + - + +
146C LEU* 3.7 8.7 - - + +
148C THR* 1.3 72.5 - - - +
150C GLU* 1.3 63.6 + - - +
152C HIS* 3.0 14.4 + - - +
153C TYR* 3.5 14.6 + - + -
198C ALA* 3.7 31.0 - - + +
199C ILE* 3.9 28.5 - - + -
202C VAL* 3.7 28.5 - - + -
237C GLY* 4.6 2.0 - - - -
240C LEU* 3.8 15.0 - - + +
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Residues in contact with GLU 150 (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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115C ASN 3.9 0.2 - - - -
116C ARG* 3.2 32.0 - - - +
117C PRO* 3.1 3.8 - - - +
118C LEU* 2.9 42.6 + - + +
119C THR* 2.8 32.4 + - - +
146C LEU 2.8 19.3 + - - +
149C LEU* 1.3 72.8 - - - +
151C ASP* 1.3 62.8 + - - +
152C HIS 3.2 1.0 + - - -
153C TYR* 3.2 14.0 + - - +
162C ASN* 2.7 36.1 + - + +
509C EDO 3.3 16.5 - - - +
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Residues in contact with ASP 151 (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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346A ARG* 3.0 44.3 + - - +
350A ARG* 3.0 20.3 + - - -
116C ARG* 2.8 29.2 + - - -
147C MET 2.9 16.1 + - - +
148C THR* 3.1 13.2 + - - +
150C GLU* 1.3 75.0 - - - +
152C HIS* 1.3 59.6 + - + +
153C TYR 3.3 1.8 - - - +
501C EDO 5.5 0.2 - - - +
509C EDO 2.9 26.6 + - - -
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Residues in contact with HIS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ARG* 5.4 1.0 + - - -
148C THR 3.0 21.9 + - - -
149C LEU 3.0 12.4 + - - +
151C ASP* 1.3 80.7 - - + +
153C TYR* 1.3 60.5 + - - +
154C HIS* 3.8 4.3 - - - -
202C VAL* 3.8 13.9 - - + -
203C ASP* 2.9 36.9 + - + +
236C VAL* 4.5 8.2 - - + +
240C LEU* 3.5 28.9 - - + +
501C EDO 3.2 47.0 + - - -
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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