Contacts of the helix formed by residues 138 - 152 (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 PRO 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LYS 3.4 9.4 - - - +
137A ILE* 1.3 87.9 - - + +
139A VAL* 1.3 65.2 + - - +
140A ASP* 3.3 10.8 - - - +
141A THR* 3.1 25.8 + - + +
142A LEU 3.0 18.4 + - - -
248A ILE 5.2 0.9 - - - +
250A GLN* 3.9 22.2 - - + +
251A ASN* 4.6 3.6 - - - +
503A EDO 5.2 4.9 - - - +
511A DMS 3.7 22.7 - - + +
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Residues in contact with VAL 139 (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* 5.5 3.5 - - - +
127A GLN* 4.7 11.2 - - - +
132A LEU* 3.4 30.7 - - + -
137A ILE 4.6 1.1 - - - +
138A PRO* 1.3 71.0 - - - +
140A ASP* 1.3 65.7 + - + +
142A LEU* 3.2 3.5 + - - +
143A ILE* 2.9 40.3 + - + +
503A EDO 6.0 0.7 - - - +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.7 6.9 - - - +
139A VAL* 1.3 79.7 + - + +
141A THR* 1.3 58.9 + - - +
143A ILE* 3.9 8.3 - - - +
144A THR* 2.6 39.7 + - - +
245A ASN* 2.9 22.4 + - - +
511A DMS 3.0 35.7 + - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.1 29.8 + - + +
140A ASP* 1.3 78.9 - - - +
142A LEU* 1.3 57.3 + - - +
145A TYR* 2.9 30.3 + - - +
245A ASN* 2.8 38.7 + - - +
246A CYS 3.7 0.4 - - - -
247A ASP 3.6 38.6 - - - +
248A ILE* 3.8 6.1 - - - +
250A GLN* 3.9 5.2 + - - +
511A DMS 3.6 7.4 - - - +
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Residues in contact with LEU 142 (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* 4.2 18.4 - - + -
126A PHE* 3.9 48.5 - - + -
132A LEU* 3.9 20.0 - - + -
137A ILE* 3.9 9.6 - - + -
138A PRO 3.0 12.2 + - - +
139A VAL* 3.2 9.2 + - - +
141A THR* 1.3 77.2 - - - +
143A ILE* 1.3 58.0 + - - +
145A TYR* 3.4 0.9 + - + +
146A LEU* 2.9 60.1 + - + +
248A ILE* 3.6 22.6 - - + +
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Residues in contact with ILE 143 (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* 4.7 8.3 - - + -
123A HIS* 4.3 28.7 - - + +
139A VAL* 2.9 27.9 + - + +
140A ASP* 4.0 7.0 - - - +
142A LEU* 1.3 77.9 - - + +
144A THR* 1.3 63.8 + - - +
146A LEU* 3.3 6.1 + - - +
147A MET* 3.0 52.3 + - + +
349C GLU 5.4 2.7 - - - +
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Residues in contact with THR 144 (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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140A ASP* 2.6 32.0 + - - +
143A ILE* 1.3 73.8 - - - +
145A TYR* 1.3 62.7 + - - +
147A MET* 4.0 6.9 - - - +
148A THR* 2.7 32.1 + - - +
244A GLU 3.7 23.3 - - - +
245A ASN* 3.5 20.2 + - + +
246A CYS* 3.9 6.1 - - - -
350C ARG* 4.4 29.6 + - + +
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Residues in contact with TYR 145 (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* 6.1 0.4 - - + -
141A THR 2.9 15.1 + - - +
142A LEU 3.9 0.7 - - - +
144A THR* 1.3 78.7 - - - +
146A LEU* 1.3 63.8 + - + +
148A THR* 3.1 2.5 + - - -
149A LEU* 2.7 57.3 + - + +
195A PHE* 3.4 32.3 - + - -
199A ILE* 3.6 10.0 - - - +
237A GLY 2.7 28.6 + - - -
240A LEU* 3.9 20.2 - - + -
241A LEU* 3.8 20.4 - - + -
246A CYS* 3.4 35.4 - - + +
248A ILE* 3.7 20.0 - - + -
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Residues in contact with LEU 146 (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* 4.9 4.6 - - + +
119A THR* 3.5 38.9 + - + +
122A MET* 3.7 45.1 - - + -
123A HIS* 3.9 9.2 - - + +
142A LEU* 2.9 47.6 + - + +
143A ILE* 3.8 5.2 - - - +
145A TYR* 1.3 89.8 - - + +
147A MET* 1.3 57.5 + - - +
149A LEU* 3.2 9.4 + - + +
150A GLU* 2.7 32.6 + - - +
248A ILE* 6.2 0.2 - - + -
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Residues in contact with MET 147 (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 28.0 - - - +
119A THR* 3.6 16.8 - - + +
143A ILE* 3.0 39.4 + - + +
144A THR* 4.0 5.2 - - - +
146A LEU* 1.3 76.4 - - - +
148A THR* 1.3 58.1 + - - +
150A GLU* 3.3 1.2 + - - +
151A ASP* 2.8 39.1 + - - +
349C GLU* 3.6 56.1 - - + +
350C ARG* 4.5 12.8 - - + +
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Residues in contact with THR 148 (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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144A THR 2.7 21.8 + - - -
145A TYR* 3.4 5.2 - - - -
147A MET* 1.3 73.6 - - - +
149A LEU* 1.3 65.3 + - - +
151A ASP* 3.3 2.1 + - - +
152A HIS* 2.9 29.3 + - - -
240A LEU* 3.9 26.7 - - + -
243A GLU* 3.5 24.1 + - - +
246A CYS* 3.5 15.7 - - - -
514A EDO 3.9 8.3 - - - -
350C ARG* 3.3 26.4 + - - +
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.7 16.6 - - + -
145A TYR* 2.7 50.4 + - + +
146A LEU* 3.5 10.5 - - + +
148A THR* 1.3 71.7 - - - +
150A GLU* 1.3 65.0 + - - +
152A HIS* 3.0 13.9 + - - +
153A TYR* 3.5 11.4 + - + -
198A ALA* 3.6 29.2 - - + +
199A ILE* 3.8 23.3 - - + -
202A VAL* 3.8 25.8 - - + -
237A GLY* 4.6 1.3 - - - -
240A LEU* 3.9 13.0 - - + +
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Residues in contact with GLU 150 (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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115A ASN 3.9 0.7 - - - +
116A ARG* 3.3 34.3 + - - +
117A PRO* 3.1 3.6 - - - +
118A LEU* 2.8 42.3 + - + +
119A THR* 2.8 32.3 + - - +
146A LEU 2.7 19.7 + - - +
149A LEU* 1.3 74.8 - - - +
151A ASP* 1.3 60.5 + - - +
153A TYR* 3.1 15.8 + - - +
162A ASN* 2.8 34.0 + - + +
504A PEG 2.9 20.9 + - - +
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Residues in contact with ASP 151 (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* 2.9 28.2 + - - -
147A MET 2.8 22.1 + - - +
148A THR* 3.5 7.0 - - - +
150A GLU* 1.3 72.0 - - - +
152A HIS* 1.3 64.6 + - + +
153A TYR 3.4 2.4 - - - +
504A PEG 3.1 44.0 + - - +
514A EDO 5.3 0.2 - - - +
346C ARG* 3.0 26.4 + - - +
350C ARG* 2.8 29.4 + - - +
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Residues in contact with HIS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR 2.9 23.7 + - - -
149A LEU 3.0 6.2 + - - +
151A ASP* 1.3 80.3 - - + +
153A TYR* 1.3 60.2 + - - +
154A HIS* 3.6 4.6 - - - -
202A VAL* 3.6 20.4 - - + -
203A ASP* 2.9 35.6 + - + +
236A VAL* 4.6 8.2 - - + +
240A LEU* 3.5 31.6 - - + +
514A EDO 3.1 41.8 - - - -
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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