Contacts of the helix formed by residues 134 - 142 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 4.6 16.6 - - + -
95B SER 4.7 0.2 - - - +
96B THR* 4.2 20.0 - - + -
109B TRP* 4.3 21.8 - - + -
131B LEU* 3.5 33.4 - - + +
132B GLY 2.8 13.6 + - - +
133B PRO* 1.3 71.2 - - - +
135B TYR* 1.3 69.3 + - + +
136B GLY 3.7 4.5 - - - +
137B PHE* 3.4 2.5 + - - +
138B GLN* 3.0 28.6 + - - +
181B ALA 6.0 0.2 - - - -
190B MET* 4.4 17.7 - - + -
191B ALA* 4.8 3.8 - - + +
192B LEU 5.1 4.5 - - - +
194B PRO* 6.2 1.8 - - - -
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Residues in contact with TYR 135 (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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91B PHE* 3.6 39.0 - + + -
109B TRP* 4.3 24.5 - + - -
134B VAL* 1.3 78.5 - - + +
136B GLY* 1.3 67.7 + - - +
137B PHE 2.9 0.5 + - - -
138B GLN* 3.0 4.0 + - - +
139B TRP* 2.7 44.5 + + + +
181B ALA* 3.6 16.8 - - + -
192B LEU* 6.4 0.4 - - + -
194B PRO* 3.5 25.3 - - + +
195B CYS* 2.9 28.9 + - - +
196B HIS* 2.9 47.7 + + + -
230B TYR* 4.7 3.4 - - - -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.2 33.6 - - - -
94B GLY* 3.6 26.5 - - - -
95B SER 4.1 6.0 + - - -
134B VAL* 3.7 4.6 - - - +
135B TYR* 1.3 78.2 - - - +
137B PHE* 1.3 61.0 + - - +
139B TRP* 3.5 3.6 + - - +
140B ARG* 3.2 17.8 + - - +
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Residues in contact with PHE 137 (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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94B GLY 4.5 3.1 - - - -
96B THR* 3.7 22.4 - - + +
133B PRO* 3.3 25.8 - - + -
134B VAL 3.4 7.1 + - - +
135B TYR 3.0 0.6 - - - -
136B GLY* 1.3 73.1 - - - +
138B GLN* 1.3 73.6 + - - +
139B TRP 3.1 1.8 - - - -
141B HIS* 2.8 57.0 + + + +
143B GLY 5.3 0.7 - - - -
144B ALA* 3.3 37.7 - - + -
146B TYR* 3.6 31.2 - + + -
153B TYR* 3.5 37.7 - + - -
186B ASP* 4.2 3.8 - - - -
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Residues in contact with GLN 138 (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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133B PRO 3.1 20.8 + - - +
134B VAL 3.0 17.1 + - - +
135B TYR* 3.0 4.3 + - - +
137B PHE* 1.3 94.7 - - - +
139B TRP* 1.3 60.6 + - - +
142B PHE* 3.3 29.2 - - + +
143B GLY 4.4 0.2 + - - -
160B GLN* 2.9 24.6 + - - -
181B ALA* 3.9 36.3 - - + +
183B ASN* 3.2 27.2 + - + +
186B ASP* 2.9 28.7 + - - +
190B MET* 4.7 3.1 - - + +
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Residues in contact with TRP 139 (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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88B LEU* 4.0 21.1 - - + -
91B PHE* 3.8 38.6 - + + +
92B ILE* 4.5 5.2 - - + -
135B TYR* 2.7 44.4 + + + +
136B GLY* 3.7 6.3 - - - +
138B GLN* 1.3 78.6 - - - +
140B ARG* 1.3 65.8 + - + +
160B GLN* 3.1 24.3 + - - +
161B LEU* 3.1 23.6 + - + -
179B MET* 3.7 39.1 + - + +
180B CYS 5.5 0.4 - - - -
181B ALA* 4.2 15.9 - - + +
230B TYR* 3.7 26.1 + + - -
233B LEU* 3.8 24.7 - - + -
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Residues in contact with ARG 140 (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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91B PHE 4.6 0.4 - - - +
92B ILE* 2.8 42.8 + - - +
93B LYS 5.1 0.9 - - - +
94B GLY* 4.3 6.5 - - - -
136B GLY 3.2 13.2 + - - +
139B TRP* 1.3 93.5 - - + +
141B HIS* 1.3 91.8 + - + +
156B GLN 3.8 2.8 - - - +
158B VAL 3.7 6.3 - - - -
159B ASP* 2.5 57.3 + - - +
161B LEU* 3.5 29.8 - - - +
162B GLN* 4.2 10.9 - - - +
288B ILE* 4.2 4.0 - - - +
289B ASP* 3.6 30.2 + - - -
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Residues in contact with HIS 141 (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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93B LYS 5.8 0.4 + - - -
94B GLY* 5.2 8.1 - - - -
136B GLY 4.6 1.1 - - - -
137B PHE* 2.8 45.9 + + + +
140B ARG* 1.3 106.2 + - + +
142B PHE* 1.3 67.1 - - - +
143B GLY 3.1 0.7 + - - -
144B ALA* 3.0 21.4 + - + +
153B TYR* 2.9 50.1 + + + +
154B SER* 4.3 5.2 - - - -
155B GLY 5.1 0.9 - - - -
156B GLN 3.3 16.5 + - - +
157B GLY* 3.6 3.4 - - - -
158B VAL 4.0 0.4 - - - -
159B ASP* 5.8 0.2 - - - -
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Residues in contact with PHE 142 (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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142A PHE* 4.4 10.8 - + - -
182A TRP 4.6 1.1 - - - -
183A ASN* 3.6 16.2 - - - -
184A PRO* 3.4 37.5 - - + -
185A ARG* 4.3 9.7 - - + +
137B PHE 3.6 2.4 + - - -
138B GLN* 3.3 34.4 + - - +
141B HIS* 1.3 73.3 - - - +
143B GLY* 1.3 62.6 + - - +
157B GLY* 3.2 4.0 - - - -
158B VAL* 2.9 42.1 + - + +
160B GLN* 3.5 23.6 - - - +
180B CYS* 3.7 12.8 - - + -
182B TRP 4.2 7.9 - - - -
183B ASN* 3.5 37.0 - - + -
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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