Contacts of the helix formed by residues 116 - 129 (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 ARG 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A ARG* 4.6 4.6 - - - +
349A GLU* 3.1 38.7 + - - +
113C SER* 3.1 28.8 + - - +
114C GLY 3.3 4.2 + - - +
115C ASN* 1.3 84.0 + - - +
117C PRO* 1.3 64.8 - - - +
118C LEU 3.2 2.8 + - - -
119C THR* 3.3 13.5 + - + -
120C VAL* 3.1 26.3 + - + +
147C MET* 3.0 37.4 + - + +
150C GLU* 3.2 29.9 - - - +
151C ASP* 2.8 29.7 + - - -
509C EDO 4.9 2.1 + - - -
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Residues in contact with PRO 117 (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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106C VAL* 4.5 4.9 - - + +
109C ILE* 4.2 1.8 - - + -
110C ALA* 3.8 34.8 - - + +
113C SER* 3.4 5.5 - - - +
115C ASN* 3.3 8.1 - - - +
116C ARG* 1.3 90.8 - - - +
118C LEU* 1.3 57.4 + - - +
120C VAL* 4.0 6.1 - - + -
121C ILE* 2.8 44.4 + - + +
150C GLU* 3.1 11.0 - - - +
162C ASN* 3.5 11.7 - - - +
163C ILE* 4.1 17.3 - - + +
166C ALA* 3.9 12.1 - - + -
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO* 1.3 78.4 - - - +
119C THR* 1.3 58.2 + - - +
121C ILE* 4.8 0.4 - - - -
122C MET* 2.9 55.2 + - + +
146C LEU* 5.2 3.4 - - + +
149C LEU* 4.0 19.1 - - + -
150C GLU* 2.9 34.6 + - + +
153C TYR* 3.9 28.9 - - + -
162C ASN* 4.0 8.7 - - + +
165C ALA* 4.0 10.5 - - + -
166C ALA* 3.8 28.3 - - - +
169C VAL* 4.1 7.9 - - + -
198C ALA* 4.1 4.9 - - + +
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Residues in contact with THR 119 (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 ARG* 3.8 13.6 - - + -
117C PRO 3.3 0.2 - - - -
118C LEU* 1.3 77.0 - - - +
120C VAL* 1.3 62.6 + - + +
123C HIS* 2.9 35.2 + - + +
143C ILE* 4.7 12.1 - - + +
146C LEU* 3.5 42.9 + - + +
147C MET* 3.6 24.3 + - + -
150C GLU* 2.8 21.2 + - - -
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Residues in contact with VAL 120 (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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92C LEU* 4.7 11.0 - - + -
96C LEU* 4.1 16.6 - - + -
109C ILE* 3.7 26.2 - - + -
113C SER* 4.1 17.3 - - - -
116C ARG* 3.1 24.9 + - + +
117C PRO* 3.6 4.3 - - + +
119C THR* 1.3 77.8 - - + +
121C ILE* 1.3 56.5 + - - +
123C HIS* 3.5 5.5 + - - +
124C THR* 2.7 38.9 + - - -
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Residues in contact with ILE 121 (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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96C LEU* 4.3 9.2 - - + -
99C VAL* 5.0 2.7 - - + -
104C LEU* 3.9 15.7 - - + -
106C VAL* 3.7 30.3 - - + -
109C ILE* 4.1 22.9 - - + -
117C PRO* 2.8 27.6 + - + +
118C LEU 4.4 0.9 - - - +
120C VAL* 1.3 70.4 - - - +
122C MET* 1.3 59.9 + - + +
124C THR* 3.5 6.6 + - - -
125C ILE* 3.0 47.3 + - + +
166C ALA* 3.8 17.9 - - + +
169C VAL* 4.5 3.4 - - + -
170C GLN* 4.0 17.5 - - + -
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Residues in contact with MET 122 (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* 2.9 41.2 + - + +
121C ILE* 1.3 72.8 - - - +
123C HIS* 1.3 60.8 + - - +
125C ILE* 3.3 3.4 + - - -
126C PHE* 2.8 61.9 + - + -
142C LEU* 5.7 0.4 - - + -
145C TYR* 6.0 0.7 - - + -
146C LEU* 3.7 30.3 - - + -
149C LEU* 5.6 0.4 - - + -
169C VAL* 3.6 29.8 - - + -
194C ILE* 3.8 18.8 - - + +
195C PHE* 4.7 10.8 - - + -
198C ALA* 3.5 18.2 - - + -
248C ILE* 6.0 1.1 - - + -
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Residues in contact with HIS 123 (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 THR* 2.9 21.9 + - + +
120C VAL* 3.9 5.8 - - - +
122C MET* 1.3 75.5 - - - +
124C THR* 1.3 58.3 + - - +
126C PHE* 3.2 4.0 + - - +
127C GLN* 2.9 63.0 + - + +
132C LEU* 4.3 5.4 - - + +
139C VAL* 3.9 27.6 - - + +
142C LEU* 3.4 21.9 - - + +
143C ILE* 4.6 18.8 - - + +
146C LEU* 3.9 9.5 - - + +
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Residues in contact with THR 124 (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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96C LEU* 3.7 33.9 - - + +
99C VAL* 4.1 29.2 - - + -
120C VAL* 2.7 22.9 + - - +
121C ILE* 3.7 6.7 - - - -
122C MET 3.3 0.2 - - - -
123C HIS* 1.3 77.5 - - - +
125C ILE* 1.3 57.5 + - - +
127C GLN* 3.3 12.3 + - - +
128C GLU* 2.8 28.9 + - + +
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Residues in contact with ILE 125 (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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99C VAL* 3.6 19.5 - - + -
121C ILE* 3.0 28.1 + - + +
122C MET* 3.8 4.7 - - - +
124C THR* 1.3 74.6 - - - +
126C PHE* 1.3 60.1 + - + +
128C GLU* 3.6 6.6 - - - +
129C ARG* 2.9 29.7 + - - +
169C VAL* 3.7 22.4 - - + -
170C GLN* 3.8 11.9 - - - -
173C HIS* 3.5 45.1 - - + +
194C ILE* 3.9 28.5 - - + -
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Residues in contact with PHE 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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122C MET* 2.8 59.5 + - + +
123C HIS 3.6 4.3 - - - +
125C ILE* 1.3 71.7 - - + +
127C GLN* 1.3 60.0 + - - +
129C ARG 3.5 0.2 + - - -
130C ASP* 3.0 7.3 + - - -
131C LEU* 2.8 52.3 + - + -
132C LEU* 3.6 15.5 - - + +
137C ILE* 3.8 26.5 - - + -
142C LEU* 3.9 30.3 - - + -
191C LEU* 3.8 25.1 - - + -
194C ILE* 3.8 19.3 - - + -
195C PHE* 5.6 3.4 - - + -
248C ILE* 5.0 8.5 - - + -
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Residues in contact with GLN 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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123C HIS* 2.9 41.4 + - + +
124C THR* 3.7 13.4 - - - +
126C PHE* 1.3 75.6 - - - +
128C GLU* 1.3 60.4 + - - +
130C ASP* 2.9 22.6 + - - +
132C LEU* 3.9 17.9 - - + -
139C VAL* 5.8 1.4 - - - +
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Residues in contact with GLU 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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99C VAL* 5.1 8.5 - - + +
100C ASN* 3.2 38.2 + - - +
124C THR* 2.8 19.6 + - + +
125C ILE* 3.6 7.6 - - - +
127C GLN* 1.3 77.0 - - - +
129C ARG* 1.3 60.5 + - + +
130C ASP* 3.5 1.2 + - - +
173C HIS* 4.0 13.7 - - + +
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Residues in contact with ARG 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 ILE* 2.9 18.4 + - - +
128C GLU* 1.3 77.3 - - + +
130C ASP* 1.3 70.1 + - - +
131C LEU* 3.1 22.8 + - + +
134C THR* 4.5 2.3 + - - -
173C HIS* 2.8 51.8 + - + -
176C LEU* 3.5 20.8 - - - +
177C SER* 3.1 19.0 + - - +
187C ASP* 5.8 0.3 - - - +
190C ILE* 3.8 32.0 - - - +
194C ILE* 3.6 26.5 - - - +
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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