Contacts of the helix formed by residues 134 - 142 (chain E) in PDB entry 3HB8
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 VAL 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90E TRP* 5.1 3.1 - - + -
91E PHE* 6.5 0.4 - - + -
95E SER 5.0 2.5 - - - +
96E THR* 3.9 16.2 - - + -
109E TRP* 4.4 16.4 - - + -
131E LEU* 3.6 42.2 - - + +
132E GLY 2.7 21.6 + - - +
133E PRO* 1.3 74.5 - - - +
135E TYR* 1.3 76.7 + - + +
136E GLY 3.4 0.9 - - - +
137E PHE* 2.7 16.9 + - - +
138E GLN* 3.1 7.9 + - - -
190E MET* 3.6 13.2 - - + -
191E ALA 4.6 2.0 - - - +
192E LEU 4.2 19.3 - - - +
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Residues in contact with TYR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PHE* 3.4 38.1 - + + -
109E TRP* 4.0 28.9 - + - -
134E VAL* 1.3 74.2 - - + +
136E GLY* 1.3 66.2 + - - +
138E GLN* 2.9 9.7 + - - +
139E TRP* 2.7 40.5 + + - +
181E ALA* 4.1 13.2 - - + -
190E MET* 4.3 4.8 - - + +
192E LEU* 6.1 0.7 - - + -
194E PRO* 4.0 19.7 - - + -
195E CYS* 2.9 27.4 + - - +
196E HIS* 3.0 51.9 + + + -
230E TYR* 4.5 3.8 - - - -
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Residues in contact with GLY 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E PHE* 3.7 32.5 - - - -
94E GLY* 3.6 24.1 - - - -
95E SER 4.2 6.4 + - - -
134E VAL* 3.1 3.0 + - - +
135E TYR* 1.3 77.5 - - - +
137E PHE* 1.3 63.0 + - - +
139E TRP* 3.3 3.0 + - - +
140E ARG* 3.2 21.3 + - - +
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Residues in contact with PHE 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLY 4.4 4.5 - - - -
96E THR* 3.6 23.0 - - + +
133E PRO* 3.4 27.6 - - + -
134E VAL 2.7 15.8 + - - +
136E GLY* 1.3 71.0 - - - +
138E GLN* 1.3 61.4 + - - +
141E HIS* 2.7 62.6 + + + -
143E GLY 5.6 0.7 - - - -
144E ALA* 3.7 37.0 - - + -
146E TYR* 3.7 31.6 - + + -
153E TYR* 3.6 37.9 - + - -
186E ASP* 4.0 6.1 - - - -
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Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E PRO* 2.8 32.8 + - - +
134E VAL 3.1 5.1 + - - +
135E TYR* 2.9 9.0 + - - +
137E PHE* 1.3 84.0 - - - +
139E TRP* 1.3 63.7 + - - +
140E ARG 3.3 0.7 + - - -
142E PHE* 3.1 41.8 + - - +
143E GLY 4.6 0.2 + - - -
158E VAL 4.1 0.2 - - - +
160E GLN* 3.0 19.2 + - - -
180E CYS 4.3 1.6 - - - +
181E ALA* 3.3 36.1 - - - +
183E ASN* 3.2 19.2 + - - +
186E ASP* 3.3 28.1 + - - +
190E MET* 4.3 4.9 - - + +
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Residues in contact with TRP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 3.8 19.7 - - + -
91E PHE* 3.5 41.7 - + + -
92E ILE* 3.8 24.9 - - + -
135E TYR* 2.7 32.0 + + - +
136E GLY* 3.3 6.0 + - - +
138E GLN* 1.3 75.3 - - + +
140E ARG* 1.3 65.3 + - + +
160E GLN* 3.0 25.8 + - - +
161E LEU* 3.2 18.5 + - + -
179E MET* 3.9 30.9 + - + +
180E CYS 5.1 2.2 - - - -
181E ALA* 4.3 24.2 - - + +
199E CYS* 6.1 0.4 - - - -
230E TYR* 3.5 30.0 + + - -
233E LEU* 3.8 18.4 - - + -
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Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PHE 4.4 1.3 - - - +
92E ILE* 3.1 25.9 + - - +
93E LYS 4.8 0.9 - - - -
94E GLY* 4.3 8.3 - - - +
136E GLY 3.2 15.9 + - - +
139E TRP* 1.3 86.5 - - + +
141E HIS* 1.3 87.8 + - + +
156E GLN 4.1 1.7 - - - +
158E VAL 3.5 6.9 - - - -
159E ASP* 2.8 56.2 + - - +
161E LEU* 3.9 21.2 - - + +
162E GLN* 3.9 21.6 + - - +
288E ILE* 4.4 1.0 - - - +
289E ASP* 2.8 38.0 + - - -
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Residues in contact with HIS 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LYS 5.9 0.4 + - - -
94E GLY* 5.0 9.7 + - - -
136E GLY 5.0 0.7 - - - -
137E PHE* 2.7 53.9 + + + +
140E ARG* 1.3 98.3 + - + +
142E PHE* 1.3 65.0 + - - +
143E GLY 3.3 0.3 + - - -
144E ALA* 3.0 20.0 + - + +
153E TYR* 3.1 46.4 + + + +
154E SER* 4.4 4.9 - - - -
155E GLY 5.0 2.0 + - - -
156E GLN 3.1 15.9 + - - +
157E GLY* 3.6 4.0 - - - -
158E VAL 3.9 0.4 - - - -
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Residues in contact with PHE 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D PHE* 4.5 8.5 - + - -
182D TRP 4.7 1.6 - - - -
183D ASN* 4.2 14.6 - - - -
184D PRO* 3.3 35.9 - - + -
185D ARG* 4.5 4.4 - - + +
137E PHE* 5.7 0.2 - - - -
138E GLN* 3.1 40.5 + - - +
141E HIS* 1.3 74.5 - - - +
143E GLY* 1.3 64.9 + - - +
144E ALA 3.2 0.2 - - - -
157E GLY* 3.1 4.5 - - - -
158E VAL* 2.6 43.3 + - + +
160E GLN* 3.1 26.2 - - + +
180E CYS* 3.6 15.5 - - + -
182E TRP 4.3 9.0 - - - -
183E ASN* 3.6 33.9 - - + -
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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