Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 3MB8
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 GLU 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.6 22.0 - - + -
71A ILE* 3.4 2.4 - - - -
72A GLY 2.7 34.7 + - - +
73A CYS* 3.8 6.3 - - - -
76A THR* 3.6 11.7 - - + +
93A ARG* 3.0 31.9 + - - +
161A THR* 3.8 2.9 - - - -
186A ASP* 3.4 0.2 + - - -
187A MET* 1.3 82.1 - - - +
189A MET* 1.3 67.1 + - - +
190A SER 3.4 2.2 - - - -
191A GLY* 3.1 5.1 + - - -
192A VAL* 2.9 24.8 + - + +
280A IMH 2.5 42.5 + - - -
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Residues in contact with MET 189 (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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93A ARG* 3.7 25.6 - - + +
113A THR* 3.5 20.2 - - + +
116A ALA* 4.2 9.4 - - + -
159A GLY* 6.3 1.3 - - - -
161A THR* 3.3 3.5 + - - +
186A ASP* 3.2 22.2 + - - +
188A GLU* 1.3 76.4 - - - +
190A SER* 1.3 63.4 + - - +
192A VAL* 3.2 5.0 + - - +
193A LEU* 2.9 43.2 + - + +
204A CYS 4.7 0.2 - - - -
205A GLY* 3.5 37.2 - - - -
206A ILE 4.1 0.2 - - - +
207A LEU* 3.6 34.8 - - + -
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Residues in contact with SER 190 (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 ALA* 3.8 12.5 - - - +
118A ASN* 2.7 39.8 + - - -
120A THR* 3.5 2.8 - - - +
123A ILE* 3.6 1.6 - - - +
133A CYS* 3.3 32.0 - - - -
161A THR* 2.8 30.2 + - - -
189A MET* 1.3 73.3 - - - +
191A GLY* 1.3 58.4 + - - +
194A GLY* 2.8 26.3 + - - -
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Residues in contact with GLY 191 (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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73A CYS* 3.6 20.7 - - - -
76A THR* 5.7 1.6 - - - -
80A ILE* 5.2 1.1 - - - -
122A LEU* 4.0 6.9 - - - +
123A ILE* 3.7 14.5 - - - +
188A GLU 3.1 6.9 + - - -
190A SER* 1.3 79.9 + - - +
192A VAL* 1.3 59.1 + - - +
195A LEU* 2.9 35.5 + - - +
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Residues in contact with VAL 192 (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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26A ILE* 3.9 23.6 - - + -
76A THR* 3.7 25.6 - - + -
80A ILE* 4.0 11.7 - - + -
91A ILE* 4.4 4.3 - - + -
93A ARG* 3.9 29.6 - - + +
188A GLU 2.9 17.8 + - - +
189A MET* 3.7 11.4 - - - +
191A GLY* 1.3 74.9 - - - +
193A LEU* 1.3 58.5 + - + +
195A LEU* 4.3 0.2 - - - +
196A CYS* 2.9 40.0 + - - +
203A THR* 3.9 14.4 - - - +
204A CYS 5.1 0.2 - - - +
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Residues in contact with LEU 193 (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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113A THR 4.3 3.6 - - - +
115A ALA* 3.9 22.0 - - - +
116A ALA* 4.1 2.2 - - + +
133A CYS 3.5 21.1 - - - +
134A VAL 3.7 17.9 - - - +
135A ALA* 4.1 7.0 - - + +
189A MET* 2.9 42.1 + - + +
190A SER 4.2 0.7 - - - +
192A VAL* 1.3 73.8 - - + +
194A GLY* 1.3 58.8 + - - +
197A GLN* 3.0 36.6 + - - +
203A THR* 3.7 19.8 - - + +
204A CYS* 3.7 35.4 - - - -
205A GLY 4.0 2.5 - - - +
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Residues in contact with GLY 194 (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 ILE* 3.8 8.1 - - - -
127A LEU* 3.6 20.6 - - - +
131A PHE* 4.6 2.0 - - - -
133A CYS* 4.0 15.3 - - - +
190A SER 2.8 21.7 + - - -
193A LEU* 1.3 74.2 - - - +
195A LEU* 1.3 61.1 + - - +
197A GLN* 3.4 7.3 + - - +
198A ALA 3.0 17.5 + - - -
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Residues in contact with LEU 195 (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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77A SER* 3.8 36.6 - - - +
80A ILE* 3.8 31.4 - - + -
81A GLU* 3.9 22.2 - - + +
122A LEU* 4.7 5.2 - - + -
123A ILE* 3.8 3.3 - - + +
126A ILE* 3.7 28.0 - - + -
191A GLY 2.9 19.8 + - - +
192A VAL 4.3 0.4 - - - +
194A GLY* 1.3 71.3 - - - +
196A CYS* 1.3 65.8 + - - +
198A ALA* 3.1 5.0 + - + +
199A ARG* 3.0 42.3 + - + +
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Residues in contact with CYS 196 (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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80A ILE* 4.2 13.5 - - - -
91A ILE* 3.8 36.3 - - - -
192A VAL 2.9 24.7 + - - +
195A LEU* 1.3 76.8 - - - +
197A GLN* 1.3 62.6 + - - +
199A ARG* 3.2 3.7 + - - +
200A GLY 3.0 5.0 + - - -
201A ILE* 2.8 46.4 + - + +
203A THR* 3.5 29.6 - - - -
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Residues in contact with GLN 197 (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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131A PHE* 4.1 22.2 - - + -
134A VAL* 2.9 38.9 + - + +
135A ALA 3.7 10.7 + - - -
136A THR* 3.7 22.8 + - - +
137A PRO* 5.6 0.2 - - - +
193A LEU 3.0 26.6 + - - +
194A GLY 3.6 5.2 - - - +
196A CYS* 1.3 77.0 - - - +
198A ALA* 1.3 61.7 + - - +
200A GLY* 3.3 12.6 + - - -
201A ILE 4.1 3.3 + - - +
203A THR* 4.4 3.0 - - + +
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Residues in contact with ALA 198 (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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126A ILE* 5.3 2.0 - - + -
127A LEU* 3.8 26.2 - - + -
131A PHE* 5.2 2.0 - - - -
194A GLY 3.0 13.8 + - - +
195A LEU* 3.1 13.4 + - + +
197A GLN* 1.3 77.2 - - - +
199A ARG* 1.3 80.5 + - - +
200A GLY 3.3 0.9 + - - -
170B ILE* 4.5 16.3 - - + +
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Residues in contact with ARG 199 (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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80A ILE* 5.2 2.9 - - + -
81A GLU* 2.8 40.0 + - - +
84A ALA* 4.8 12.4 - - + +
126A ILE* 5.4 5.5 - - - +
195A LEU* 3.0 34.4 + - + +
196A CYS 4.0 2.2 - - - +
198A ALA* 1.3 102.3 + - - +
200A GLY* 1.3 63.0 + - - +
201A ILE* 3.3 22.3 + - + +
168B ASN* 3.1 41.2 + - - +
169B GLY 6.1 0.2 - - - -
170B ILE* 5.0 8.1 - - - +
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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