Contacts of the helix formed by residues 116 - 129 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B SER* 3.0 27.1 + - - +
114B GLY 3.2 9.0 - - - +
115B ASN* 1.3 83.5 + - - +
117B PRO* 1.4 65.4 - - - +
118B LEU 3.2 0.3 + - - -
119B THR* 3.3 18.4 + - - -
120B VAL* 3.2 19.3 + - + +
147B MET* 3.0 34.7 + - - +
150B GLU* 3.1 34.4 + - - +
151B ASP* 2.9 31.8 + - - -
346D ARG* 4.7 2.8 - - - +
349D GLU* 2.7 45.0 + - - +
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.2 8.1 - - + +
109B ILE* 4.0 9.2 - - + -
110B ALA* 3.6 38.6 - - + +
113B SER* 3.9 0.6 - - - -
115B ASN* 3.3 7.2 - - - -
116B ARG* 1.4 88.1 - - - +
118B LEU* 1.3 62.2 + - - +
120B VAL* 3.8 8.3 - - + -
121B ILE* 3.0 30.3 + - - +
150B GLU* 3.1 9.2 - - - +
162B ASN* 3.4 13.5 - - - +
163B ILE* 4.1 16.8 - - + -
166B ALA* 3.7 9.6 - - + -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PRO* 1.3 74.7 - - - +
119B THR* 1.3 62.0 + - - +
122B MET* 3.1 49.0 + - + +
146B LEU* 4.6 2.9 - - + +
149B LEU* 3.8 28.9 - - + -
150B GLU* 2.8 45.3 + - + +
153B TYR* 4.2 9.4 - - + -
162B ASN* 4.0 9.9 - - + +
165B ALA* 4.0 5.6 - - + -
166B ALA* 3.6 28.5 - - - +
169B VAL* 3.9 12.1 - - + -
198B ALA* 4.1 9.0 - - + +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.3 18.9 + - - -
118B LEU* 1.3 79.8 - - - +
120B VAL* 1.3 63.5 + - + +
123B HIS* 3.0 28.2 + - - +
143B ILE* 4.1 19.5 - - + -
146B LEU* 3.4 26.1 - - + +
147B MET* 3.5 31.0 + - + -
150B GLU* 2.6 22.8 + - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 5.0 8.7 - - + -
96B LEU* 4.0 16.7 - - + +
109B ILE* 3.9 16.4 - - + -
113B SER* 3.3 24.9 - - - +
116B ARG* 3.2 16.2 - - + +
117B PRO* 3.6 11.4 - - + +
119B THR* 1.3 81.7 - - + +
121B ILE* 1.3 60.8 + - - +
123B HIS* 3.9 7.0 - - - +
124B THR* 2.7 35.2 + - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 4.2 16.2 - - + -
99B VAL* 4.6 3.6 - - + -
104B LEU* 4.0 21.8 - - + -
106B VAL* 4.0 26.7 - - + -
109B ILE* 4.0 14.4 - - + -
117B PRO 3.0 22.4 + - - +
118B LEU 4.4 0.4 - - - +
120B VAL* 1.3 75.4 - - - +
122B MET* 1.3 67.6 + - - +
124B THR* 3.3 4.1 + - - -
125B ILE* 2.9 46.4 + - + +
166B ALA* 4.1 13.0 - - + +
169B VAL* 4.1 9.4 - - + -
170B GLN* 4.0 15.3 - - + -
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.1 38.6 + - + +
121B ILE* 1.3 78.4 - - - +
123B HIS* 1.3 52.4 + - - +
125B ILE* 3.3 2.9 + - - +
126B PHE* 2.7 70.1 + - + -
145B TYR* 6.1 0.9 - - + -
146B LEU* 3.6 34.1 - - + -
149B LEU* 5.5 0.4 - - + -
169B VAL* 3.5 24.9 - - + -
194B ILE* 3.9 16.4 - - + +
195B PHE* 4.7 7.4 - - + -
198B ALA* 3.5 25.8 - - + -
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR 3.0 20.5 + - - +
120B VAL* 4.0 7.4 - - - +
121B ILE 3.2 0.2 - - - -
122B MET* 1.3 76.3 - - - +
124B THR* 1.3 56.9 + - - +
126B PHE* 3.1 6.3 + - - +
127B GLN* 2.8 67.8 + - + +
132B LEU* 5.2 0.2 - - + -
139B VAL* 4.5 14.6 - - + -
142B LEU* 4.0 13.0 - - + +
143B ILE* 3.8 32.4 - - + +
146B LEU* 3.8 4.7 - - + +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 3.7 32.0 - - + +
99B VAL* 3.9 29.6 - - + -
120B VAL 2.7 22.3 + - - -
121B ILE* 3.6 5.4 - - - -
123B HIS* 1.3 81.0 - - - +
125B ILE* 1.3 58.6 + - - +
127B GLN* 3.4 6.4 + - - +
128B GLU* 3.0 29.8 + - + +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.7 18.8 - - + -
121B ILE* 2.9 40.6 + - + +
122B MET* 3.6 4.5 - - - +
124B THR* 1.3 73.6 - - - +
126B PHE* 1.3 61.3 + - + +
128B GLU* 3.3 6.9 + - - +
129B ARG* 3.0 32.7 + - - +
131B LEU* 5.2 0.2 - - + -
169B VAL* 3.7 16.8 - - + -
170B GLN* 4.0 4.9 - - - -
173B HIS* 3.5 47.1 - - + +
194B ILE* 4.0 26.7 - - + -
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 2.7 63.2 + - + +
123B HIS 3.5 4.0 - - - +
125B ILE* 1.3 75.1 - - + +
127B GLN* 1.3 67.7 + - - +
129B ARG 3.5 0.2 + - - -
130B ASP 3.2 2.1 + - - -
131B LEU* 3.1 49.0 + - + -
132B LEU* 3.5 16.3 - - + +
137B ILE* 4.1 15.5 - - + -
142B LEU* 3.9 35.4 - - + -
191B LEU* 3.7 31.0 - - + -
194B ILE* 3.9 14.4 - - + -
195B PHE* 5.6 3.1 - + + -
248B ILE* 5.3 7.0 - - + -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B HIS* 2.8 49.9 + - + +
124B THR* 3.9 6.5 - - - +
126B PHE* 1.3 69.7 - - - +
128B GLU* 1.3 57.6 + - + +
130B ASP* 2.5 32.8 + - - +
132B LEU* 3.7 18.5 - - - +
139B VAL* 4.0 15.5 - - - +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 5.3 4.0 - - + -
100B ASN* 4.1 26.5 + - - +
124B THR* 3.0 20.6 + - + +
125B ILE* 3.3 3.0 + - - +
127B GLN* 1.3 79.8 - - + +
129B ARG* 1.3 74.4 + - - +
130B ASP* 3.3 0.9 - - - +
173B HIS* 3.4 15.2 - - - -
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.0 16.1 + - - +
127B GLN 3.0 0.6 - - - -
128B GLU* 1.3 89.7 - - - +
130B ASP* 1.3 71.1 + - - +
131B LEU* 3.0 23.1 + - + +
134B THR* 4.2 2.6 + - - -
173B HIS* 2.9 36.2 + - - -
176B LEU* 3.4 18.0 + - - +
177B SER* 2.7 28.6 + - - +
187B ASP* 5.6 1.9 - - - +
190B ILE* 3.4 40.9 - - - +
194B ILE* 3.8 20.2 - - - +
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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