Contacts of the helix formed by residues 116 - 129 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A SER* 3.1 27.6 + - - +
114A GLY 4.1 5.2 - - - +
115A ASN* 1.3 83.4 + - - +
117A PRO* 1.4 65.1 - - - +
118A LEU 3.3 2.5 - - - -
119A THR* 3.5 15.4 + - - -
120A VAL* 3.1 27.1 + - + +
147A MET* 3.7 24.2 + - - +
150A GLU* 3.3 45.5 + - - +
151A ASP* 2.9 28.3 + - - -
504A PEG 4.8 3.2 + - - -
346C ARG* 4.7 1.6 - - - +
349C GLU* 2.6 44.3 + - - +
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 4.6 4.7 - - + +
109A ILE* 4.2 7.2 - - + -
110A ALA* 3.8 31.0 - - + +
113A SER* 3.3 5.5 - - - +
115A ASN* 3.2 10.3 - - - +
116A ARG* 1.4 89.8 - - - +
118A LEU* 1.3 63.3 + - - +
120A VAL* 4.0 5.6 - - + -
121A ILE* 3.0 33.1 + - + +
150A GLU* 3.1 7.0 - - - +
162A ASN* 3.3 16.6 - - - +
163A ILE* 4.1 16.8 - - + -
166A ALA* 3.7 12.1 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 1.3 70.7 - - - +
119A THR* 1.3 61.2 + - - +
121A ILE* 4.9 0.2 - - - -
122A MET* 2.9 54.0 + - + +
146A LEU* 5.1 2.7 - - + +
149A LEU* 3.7 31.6 - - + -
150A GLU* 2.8 32.5 + - + +
153A TYR* 3.8 19.5 - - + -
162A ASN* 4.0 9.2 - - + +
165A ALA* 3.9 5.8 - - + -
166A ALA* 3.8 27.1 - - - +
169A VAL* 3.9 13.0 - - + -
198A ALA* 3.8 12.1 - - + +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ARG* 3.7 14.0 - - - -
117A PRO 3.4 0.2 - - - -
118A LEU* 1.3 76.6 - - - +
120A VAL* 1.3 63.4 + - + +
123A HIS* 2.9 34.4 + - + +
143A ILE* 4.7 10.5 - - + +
146A LEU* 3.5 45.2 - - + +
147A MET* 3.5 25.4 + - + -
150A GLU* 2.8 23.2 + - - -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.2 16.4 - - + -
96A LEU* 4.6 12.3 - - + -
109A ILE* 3.8 24.0 - - + -
113A SER* 4.0 17.3 - - - -
116A ARG* 3.1 23.7 + - + +
117A PRO* 3.6 4.9 - - + +
119A THR* 1.3 80.8 - - + +
121A ILE* 1.3 59.1 + - + +
123A HIS* 3.4 6.3 + - - +
124A THR* 2.7 38.5 + - - -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.1 20.6 - - + -
99A VAL* 4.7 2.5 - - + -
104A LEU* 3.9 23.3 - - + -
106A VAL* 3.9 13.5 - - + -
109A ILE* 4.1 12.6 - - + -
117A PRO 3.0 22.8 + - - +
118A LEU 4.3 0.7 - - - +
120A VAL* 1.3 74.7 - - - +
122A MET* 1.3 63.7 + - - +
124A THR* 3.4 5.3 + - - -
125A ILE* 2.9 45.0 + - + +
166A ALA* 3.8 26.9 - - + +
169A VAL* 4.2 4.3 - - + -
170A GLN* 4.0 16.4 - - + -
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Residues in contact with MET 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 2.9 39.1 + - + +
121A ILE* 1.3 76.5 - - - +
123A HIS* 1.3 57.6 + - - +
125A ILE* 3.2 3.9 + - - -
126A PHE* 2.8 61.5 + - + -
142A LEU* 5.7 0.2 - - + -
145A TYR* 6.1 0.7 - - + -
146A LEU* 3.7 33.9 - - + -
149A LEU* 5.6 0.2 - - + -
169A VAL* 3.7 14.4 - - + -
194A ILE* 3.6 27.1 - - + +
195A PHE* 4.7 10.1 - - + -
198A ALA* 3.6 24.9 - - + -
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Residues in contact with HIS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 2.9 21.8 + - + +
120A VAL* 3.7 6.2 + - - +
122A MET* 1.3 76.1 - - - +
124A THR* 1.3 66.8 + - - +
126A PHE* 3.4 4.9 + - - +
127A GLN* 3.0 65.9 + - + +
132A LEU* 5.3 1.7 - - + +
139A VAL* 5.5 4.1 - - + +
142A LEU* 4.2 18.2 - - + -
143A ILE* 4.3 26.5 - - + +
146A LEU* 3.9 10.0 - - + +
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.8 27.8 - - + +
99A VAL* 4.2 29.4 - - + -
120A VAL* 2.7 23.3 + - - +
121A ILE* 3.7 6.5 - - - -
123A HIS* 1.3 81.7 + - - +
125A ILE* 1.3 59.0 + - - +
127A GLN* 3.5 4.3 + - - +
128A GLU* 2.8 30.9 + - + +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 3.9 17.0 - - + -
121A ILE* 2.9 41.0 + - + +
122A MET* 3.7 3.8 - - - +
124A THR* 1.3 73.7 - - - +
126A PHE* 1.3 62.4 + - + +
128A GLU* 3.2 6.2 + - - +
129A ARG* 2.8 33.2 + - - +
169A VAL* 3.7 17.9 - - + -
170A GLN* 4.0 5.6 - - - -
173A HIS* 3.7 43.3 - - + +
194A ILE* 3.8 31.0 - - + -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET* 2.8 55.3 + - + +
123A HIS 3.8 3.1 - - - +
125A ILE* 1.3 73.8 - - + +
127A GLN* 1.3 57.5 + - - +
129A ARG 3.5 0.2 + - - -
130A ASP* 3.0 7.4 + - - -
131A LEU* 2.8 54.3 + - + -
132A LEU* 3.8 15.7 - - + +
137A ILE* 3.7 26.5 - - + -
142A LEU* 3.9 29.6 - - + -
191A LEU* 3.6 26.9 - - + -
194A ILE* 3.9 18.4 - - + -
195A PHE* 5.6 3.6 - + + -
248A ILE* 5.1 7.6 - - + -
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A HIS* 3.0 56.5 + - + +
124A THR* 3.8 5.4 - - - +
126A PHE* 1.3 73.4 - - - +
128A GLU* 1.3 67.1 + - - +
130A ASP* 3.1 15.5 + - - +
132A LEU* 3.7 25.8 - - + +
139A VAL* 4.7 8.1 - - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 5.2 6.0 - - + +
100A ASN* 3.0 37.5 + - - +
124A THR* 2.8 25.9 + - + +
125A ILE* 3.2 8.7 + - - +
127A GLN* 1.3 74.5 - - - +
129A ARG* 1.3 60.4 + - + +
130A ASP* 3.6 1.4 + - - +
173A HIS* 4.7 10.3 - - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 2.8 17.9 + - - +
128A GLU* 1.3 77.3 - - + +
130A ASP* 1.3 68.9 + - - +
131A LEU* 3.2 21.6 + - + +
134A THR* 4.9 1.7 + - - -
173A HIS* 2.9 42.5 + - + -
176A LEU* 3.4 22.4 + - - +
177A SER* 2.9 28.1 + - - +
187A ASP* 5.2 4.0 - - - +
190A ILE* 3.8 30.6 - - + +
194A ILE* 3.6 25.4 - - - +
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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