Contacts of the helix formed by residues 138 - 152 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D LYS 3.3 10.3 - - - +
137D ILE* 1.3 88.9 - - + +
139D VAL* 1.3 65.8 + - - +
140D ASP* 3.7 13.0 - - - +
141D THR* 3.2 26.2 + - + +
142D LEU 3.0 18.2 + - - -
248D ILE 5.3 0.9 - - - +
250D GLN* 4.2 24.0 - - + +
251D ASN* 4.4 6.5 - - - +
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D HIS* 3.7 28.5 - - + +
127D GLN* 4.2 4.9 - - - +
132D LEU* 3.7 21.1 - - + -
137D ILE 3.4 2.8 + - - -
138D PRO* 1.3 71.5 - - - +
140D ASP* 1.3 66.4 + - + +
142D LEU* 3.3 2.6 + - + +
143D ILE* 2.9 40.7 + - + +
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Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B DMS 3.7 30.6 - - + +
138D PRO* 3.7 14.0 - - - +
139D VAL* 1.3 83.6 + - + +
141D THR* 1.3 59.9 + - - +
143D ILE 3.5 0.2 + - - -
144D THR* 2.8 38.8 + - - +
245D ASN* 3.1 24.6 + - - +
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ILE* 4.9 0.2 - - - -
138D PRO* 3.2 32.2 + - + +
140D ASP* 1.3 78.6 + - - +
142D LEU* 1.3 59.9 + - - +
144D THR 3.3 0.5 + - - -
145D TYR* 2.8 30.0 + - - +
245D ASN* 2.8 38.1 + - - +
246D CYS 3.8 0.2 - - - -
247D ASP 3.6 38.4 - - - +
248D ILE* 3.8 5.8 - - - +
250D GLN* 4.0 7.4 + - - +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D HIS* 4.1 18.4 - - + -
126D PHE* 3.9 51.6 - - + -
132D LEU* 4.0 17.3 - - + -
137D ILE* 3.9 9.2 - - + +
138D PRO 3.0 12.2 + - - +
139D VAL* 3.3 10.3 + - - +
141D THR* 1.3 75.9 - - - +
143D ILE* 1.3 59.6 + - + +
145D TYR* 3.4 0.9 + - + +
146D LEU* 2.9 59.1 + - + +
248D ILE* 3.7 24.1 - - + +
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B DMS 3.5 30.1 - - + -
119D THR* 4.6 4.7 - - + -
123D HIS* 4.0 27.4 - - + +
139D VAL* 2.9 36.4 + - + +
140D ASP* 4.8 0.2 - - - -
142D LEU* 1.3 76.8 - - + +
144D THR* 1.3 63.4 + - - +
146D LEU* 3.2 6.9 + - - +
147D MET* 2.9 53.5 + - + +
505D EDO 4.5 15.5 - - - +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ARG* 4.5 21.4 + - + +
512B DMS 3.6 16.2 + - - -
140D ASP* 2.8 23.0 + - - +
143D ILE* 1.3 78.4 - - - +
145D TYR* 1.3 58.1 + - - +
147D MET* 3.4 6.8 + - - +
148D THR* 2.7 36.3 + - - +
244D GLU 3.5 25.4 - - - +
245D ASN* 3.4 19.9 + - + +
246D CYS* 3.8 6.1 - - - -
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Residues in contact with TYR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D MET* 6.0 0.7 - - + -
141D THR 2.8 16.0 + - - +
142D LEU 3.8 0.4 - - - +
144D THR* 1.3 78.0 - - - +
146D LEU* 1.3 67.6 + - + +
148D THR* 3.1 2.4 + - - -
149D LEU* 2.8 51.5 + - + +
195D PHE* 3.3 32.9 - + - -
199D ILE* 3.6 10.0 - - - +
237D GLY* 2.8 20.4 + - - -
240D LEU* 3.8 21.5 - - + -
241D LEU* 3.6 26.2 - - + -
246D CYS* 3.4 36.3 - - + +
248D ILE* 3.5 22.2 - - + -
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.8 4.5 - - + +
119D THR* 3.4 39.1 + - + +
122D MET* 3.6 46.4 - - + -
123D HIS* 4.0 8.7 - - + +
142D LEU* 2.9 48.4 + - + +
143D ILE* 3.2 6.0 + - + +
145D TYR* 1.3 84.5 - - + +
147D MET* 1.3 58.6 + - - +
149D LEU* 3.7 10.7 - - + +
150D GLU* 2.8 31.5 + - - +
248D ILE* 6.2 0.2 - - + -
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Residues in contact with MET 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLU* 3.6 54.3 - - + +
350B ARG* 4.3 13.9 - - + +
512B DMS 5.1 0.4 - - - -
116D ARG* 3.8 29.4 - - - +
119D THR* 3.6 16.6 - - + +
143D ILE* 2.9 43.7 + - + +
144D THR* 3.9 5.2 - - - +
146D LEU* 1.3 76.5 - - - +
148D THR* 1.3 53.2 + - - +
150D GLU* 3.4 1.0 + - - +
151D ASP* 2.8 44.6 + - - +
505D EDO 4.8 6.1 - - - +
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Residues in contact with THR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ARG* 3.3 27.5 + - - +
144D THR 2.7 21.5 + - - -
145D TYR 3.4 4.9 - - - -
147D MET* 1.3 76.9 - - - +
149D LEU* 1.3 63.2 + - - +
151D ASP* 3.1 8.6 + - - +
152D HIS* 2.9 23.4 + - - -
240D LEU* 4.0 25.1 - - + -
243D GLU* 3.4 13.2 + - - +
246D CYS* 3.6 15.4 - - - -
501D EDO 3.3 21.1 - - - +
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.0 13.5 - - + -
145D TYR* 2.8 43.2 + - + +
146D LEU* 3.7 9.2 - - + +
148D THR* 1.3 77.3 - - - +
150D GLU* 1.3 63.8 + - - +
152D HIS* 2.9 15.8 + - - +
153D TYR* 3.5 11.6 - - + -
198D ALA* 3.8 33.9 - - + +
199D ILE* 3.9 25.8 - - + -
202D VAL* 3.6 31.2 - - + -
237D GLY* 4.7 1.3 - - - -
240D LEU* 3.8 13.0 - - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ASN 3.9 0.2 - - - -
116D ARG* 3.3 31.9 + - - +
117D PRO* 3.1 5.0 - - - +
118D LEU* 3.0 41.3 + - + +
119D THR* 2.7 35.5 + - - -
146D LEU 2.8 21.0 + - - +
149D LEU* 1.3 74.8 - - - +
151D ASP* 1.3 60.3 + - - +
152D HIS 3.0 1.3 + - - -
153D TYR* 3.2 9.1 + - - +
162D ASN* 2.9 30.3 + - + -
508D DMS 3.1 30.3 - - - +
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Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ARG* 2.9 37.8 + - - +
350B ARG* 2.8 29.9 + - - +
116D ARG* 2.9 25.3 + - - -
147D MET 2.8 20.4 + - - +
148D THR* 3.1 10.7 + - - +
150D GLU* 1.3 73.2 - - - +
152D HIS* 1.3 63.9 + - + +
153D TYR 3.4 2.3 - - - +
508D DMS 3.3 28.4 + - + +
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Residues in contact with HIS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ARG* 6.0 0.4 - - - -
148D THR 2.9 19.9 + - - +
149D LEU 2.9 10.8 + - - +
151D ASP* 1.3 82.4 - - + +
153D TYR* 1.3 59.9 + - - +
154D HIS* 3.6 5.8 - - - -
202D VAL* 3.6 17.3 - - + -
203D ASP* 2.8 34.8 + - + +
236D VAL* 4.6 8.3 - - + -
240D LEU* 3.7 30.1 - - + +
243D GLU* 4.2 1.4 + - - -
501D EDO 3.1 39.8 + - - -
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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