Contacts of the helix formed by residues 137 - 148 (chain B) in PDB entry 2B9R
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 LEU 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU* 4.6 8.3 - - + +
60B TYR* 4.0 18.6 - - + -
61B MET* 4.1 35.0 - - + +
64B SER* 4.7 1.6 - - - -
95B GLU* 4.5 16.4 - - - +
135B ARG* 3.1 49.5 + - + +
136B PRO* 1.3 73.9 - - - +
138B PRO* 1.3 65.4 - - + +
139B LEU* 3.2 5.4 - - + +
140B HIS* 2.8 65.7 + - + +
141B PHE* 3.5 7.3 + - - -
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Residues in contact with PRO 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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60B TYR* 4.2 23.1 - - + -
135B ARG* 4.4 2.9 - - - +
137B LEU* 1.3 93.3 - - + +
139B LEU* 1.3 53.1 + - - +
141B PHE* 2.9 10.2 + - + +
142B LEU* 2.8 33.6 + - - +
163B MET* 3.7 31.9 - - + +
177B PRO* 3.8 33.0 - - + -
178B SER 5.0 0.9 - - - +
180B ILE* 5.2 9.2 - - + -
181B ALA* 4.2 1.6 - - + +
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Residues in contact with LEU 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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56B GLN* 3.7 17.7 - - + -
57B GLU* 3.6 49.6 - - + +
60B TYR* 3.5 19.5 - - + -
137B LEU* 3.2 1.3 - - + +
138B PRO* 1.3 78.7 - - - +
140B HIS* 1.3 62.5 + - + +
142B LEU* 3.7 3.3 - - + +
143B ARG* 2.7 77.9 + - - +
160B LYS* 4.9 8.5 - - + +
163B MET* 3.7 16.5 - - + +
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Residues in contact with HIS 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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14B LEU* 4.9 24.4 - - + +
57B GLU* 4.9 12.3 - - + +
95B GLU* 5.7 4.3 - - - -
136B PRO* 4.8 2.2 - - + +
137B LEU* 2.8 61.6 + - + +
139B LEU* 1.3 83.4 - - + +
141B PHE* 1.3 64.1 + - + +
143B ARG* 3.6 6.9 + - - +
144B ARG* 3.2 18.9 + - - +
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Residues in contact with PHE 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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11B TYR* 3.4 48.2 - + + -
14B LEU* 4.1 23.6 - - + -
15B ARG* 4.3 2.0 - - - -
18B GLU* 3.9 7.2 - - - -
136B PRO* 4.1 27.4 - - + -
137B LEU 3.5 7.1 + - - -
138B PRO* 2.9 5.8 + - + +
140B HIS* 1.3 76.2 - - + +
142B LEU* 1.3 66.0 + - - +
144B ARG* 3.0 8.5 + - - +
145B ALA* 2.9 21.8 + - - +
177B PRO* 3.7 17.9 - - + -
178B SER* 3.0 44.0 - - - -
181B ALA* 3.8 15.4 - - + +
205B LEU* 5.7 1.4 - - - +
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Residues in contact with LEU 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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138B PRO 2.8 15.6 + - - +
139B LEU* 3.7 8.3 - - + +
141B PHE* 1.3 76.3 - - - +
143B ARG* 1.3 65.3 + - + +
145B ALA* 2.9 14.6 + - + +
146B SER* 3.1 15.5 + - - -
156B HIS* 4.2 11.9 - - + +
159B ALA* 3.9 19.7 - - + -
160B LYS* 3.8 38.1 - - + +
163B MET* 3.6 27.8 - - + -
181B ALA* 3.9 25.9 - - + +
184B ALA* 4.9 0.7 - - + -
185B PHE* 4.3 14.8 - - + +
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Residues in contact with ARG 143 (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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56B GLN* 6.1 0.6 - - - +
57B GLU* 4.8 7.1 + - - +
139B LEU* 2.7 67.9 + - - +
140B HIS* 3.8 7.4 - - - +
142B LEU* 1.3 75.9 - - - +
144B ARG* 1.3 62.9 + - - +
146B SER* 3.3 6.5 + - - -
147B LYS* 3.1 23.1 + - - +
156B HIS* 3.8 10.8 + - - -
160B LYS* 2.1 42.2 - - - +
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Residues in contact with ARG 144 (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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10B ILE* 5.7 3.4 - - - +
11B TYR* 3.3 53.0 - - + +
140B HIS 3.2 10.6 + - - +
141B PHE* 3.0 14.6 + - + +
143B ARG* 1.3 78.3 - - - +
145B ALA* 1.3 62.1 + - - +
147B LYS* 3.2 8.0 + - + +
148B ILE* 3.1 38.2 + - + +
204B TYR* 3.0 53.0 + - - +
205B LEU* 3.9 11.4 - - + +
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Residues in contact with ALA 145 (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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141B PHE 2.9 9.5 + - - +
142B LEU* 2.9 11.9 + - + +
144B ARG* 1.3 76.2 - - - +
146B SER* 1.3 54.8 + - - +
148B ILE* 2.5 38.7 - - - +
181B ALA* 5.9 1.8 - - + +
182B ALA* 5.9 2.0 - - - -
185B PHE* 3.8 39.2 - - + -
201B LEU* 4.6 0.2 - - - +
205B LEU* 4.0 21.1 - - + +
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Residues in contact with SER 146 (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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142B LEU 3.1 6.0 + - - -
143B ARG* 3.7 7.2 - - - -
145B ALA* 1.3 77.3 - - - +
147B LYS* 1.3 63.6 + - - +
148B ILE 3.0 2.6 + - - +
149B GLY 3.8 1.3 - - - +
150B GLU 2.8 26.3 - - - +
151B VAL* 4.4 9.6 - - - +
156B HIS* 2.6 44.8 + - - +
185B PHE* 4.3 12.7 - - - -
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Residues in contact with LYS 147 (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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143B ARG 3.1 10.8 + - - +
144B ARG* 3.6 11.0 - - + +
146B SER* 1.3 80.8 - - - +
148B ILE* 1.3 60.2 + - + +
149B GLY 3.9 1.2 + - - -
150B GLU 4.4 3.3 - - - +
151B VAL* 5.2 18.0 - - - +
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Residues in contact with ILE 148 (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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144B ARG* 3.1 30.4 + - + +
145B ALA* 2.5 28.2 - - - +
147B LYS* 1.3 79.6 - - + +
149B GLY* 1.3 65.6 + - - +
200B THR 5.3 0.2 - - - +
201B LEU* 3.7 31.3 - - + +
204B TYR* 3.8 48.5 - - + -
205B LEU* 3.9 20.4 - - + -
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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