Contacts of the helix formed by residues 177 - 190 (chain B) in PDB entry 2EBJ
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 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 3.2 15.9 - - - +
175B TYR* 3.9 21.2 - - + +
176B VAL* 1.3 90.5 - - + +
178B LEU* 1.3 65.6 + - - +
179B GLU* 4.4 7.4 - - + +
180B VAL* 3.0 32.8 + - + +
181B GLN* 3.0 10.0 + - - +
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Residues in contact with LEU 178 (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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15B HIS* 5.2 1.3 - - + -
17B PRO* 3.8 20.4 - - + +
20B ALA* 3.8 26.0 - - + +
21B LEU* 3.9 15.7 - - + +
24B LEU* 3.8 23.6 - - + -
164B ASP* 3.8 22.4 - - + +
165B GLU* 2.7 23.8 + - - +
176B VAL 3.4 1.6 + - - -
177B PRO* 1.3 71.0 - - - +
179B GLU* 1.3 58.1 + - - +
181B GLN* 3.2 18.6 + - - +
182B ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.4 12.9 - - + +
165B GLU* 4.9 2.2 + - - +
177B PRO* 3.2 6.5 - - + +
178B LEU* 1.3 77.9 - - - +
180B VAL* 1.3 68.1 + - - +
182B ALA* 3.5 3.5 + - + +
183B ARG* 3.1 22.0 + - + +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.1 0.2 - - + -
126B ILE* 4.2 30.2 - - + +
127B PRO* 6.3 0.4 - - + -
176B VAL* 3.8 17.5 - - + -
177B PRO* 3.0 29.3 + - + +
179B GLU* 1.3 82.1 - - - +
181B GLN* 1.3 67.4 + - - +
183B ARG* 3.2 9.9 + - - +
184B ALA* 3.0 21.1 + - - +
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Residues in contact with GLN 181 (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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17B PRO* 4.3 2.2 - - - +
21B LEU* 3.7 10.5 - - + +
73B LEU* 4.3 10.8 - - + +
161B LEU* 3.2 40.9 - - + +
162B PRO* 2.9 29.0 + - - +
163B PRO 3.4 5.0 - - - +
164B ASP* 3.9 3.0 - - - +
176B VAL* 2.9 30.1 - - + +
177B PRO 3.0 14.4 + - - +
178B LEU* 3.5 18.7 - - - +
180B VAL* 1.3 76.1 - - - +
182B ALA* 1.3 56.3 + - - +
184B ALA* 3.2 8.9 + - - +
185B VAL* 2.9 31.7 + - - +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.8 21.7 - - + +
24B LEU* 4.0 31.4 - - + +
25B LEU* 3.9 8.9 - - + +
178B LEU 2.9 17.0 + - - +
179B GLU* 3.7 5.2 - - - +
180B VAL 3.2 0.2 - - - -
181B GLN* 1.3 74.8 - - - +
183B ARG* 1.3 59.6 + - - +
185B VAL* 3.2 3.1 + - - +
186B ARG* 2.9 29.0 + - - +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 5.4 4.8 - - - +
124B ALA* 2.9 49.5 + - - +
126B ILE* 4.2 13.0 - - + +
179B GLU* 3.1 15.6 + - + +
180B VAL* 3.2 11.8 + - - +
182B ALA* 1.3 75.3 - - - +
184B ALA* 1.3 58.0 + - - +
186B ARG* 3.3 32.1 + - - +
187B LEU* 3.0 39.1 + - + +
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Residues in contact with ALA 184 (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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73B LEU* 3.4 34.8 - - + -
121B TRP* 2.9 40.0 + - + +
126B ILE* 4.0 13.8 - - + +
159B LEU* 5.5 0.2 - - + -
180B VAL 3.0 9.3 + - - +
181B GLN 3.4 6.1 - - - +
183B ARG* 1.3 78.0 - - - +
185B VAL* 1.3 62.5 + - + +
187B LEU 3.3 0.9 + - - -
188B ALA* 2.9 13.3 + - - +
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Residues in contact with VAL 185 (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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4B VAL* 4.7 1.8 - - + -
21B LEU* 3.6 25.6 - - + -
25B LEU* 4.0 17.7 - - + -
62B LEU* 4.1 13.2 - - + -
64B LEU* 4.0 22.2 - - + -
159B LEU* 4.1 11.4 - - + -
161B LEU* 4.5 4.7 - - + -
181B GLN 2.9 19.1 + - - +
182B ALA 3.2 6.7 + - - +
184B ALA* 1.3 75.0 - - - +
186B ARG* 1.3 59.2 + - - +
188B ALA* 3.0 8.5 + - - +
189B LEU* 2.8 44.6 + - + +
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Residues in contact with ARG 186 (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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25B LEU* 4.4 7.2 - - + +
26B PRO* 4.5 20.4 - - + -
29B VAL* 4.1 15.9 - - + +
182B ALA 2.9 13.3 + - - +
183B ARG* 3.5 38.9 + - - +
185B VAL* 1.3 77.1 - - - +
187B LEU* 1.3 67.5 + - - +
189B LEU* 3.1 12.8 + - - +
190B GLU* 2.7 60.3 + - - +
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Residues in contact with LEU 187 (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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117B VAL* 5.0 0.4 - - - -
120B ARG* 3.8 39.7 - - + +
121B TRP* 3.9 23.3 - - + +
124B ALA* 3.8 29.6 - - + -
126B ILE* 4.3 6.7 - - + -
183B ARG* 3.0 26.6 + - + +
184B ALA 3.6 6.5 - - - +
186B ARG* 1.3 88.3 - - - +
188B ALA* 1.3 61.0 + - - +
190B GLU* 3.3 28.6 + - - +
191B HIS* 2.8 26.4 + - - -
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Residues in contact with ALA 188 (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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62B LEU* 4.2 12.8 - - + -
112B PHE* 4.0 21.4 - - + -
117B VAL* 3.9 25.1 - - + -
121B TRP* 4.2 0.4 - - - +
159B LEU* 4.3 10.5 - - + -
184B ALA 2.9 13.9 + - - +
185B VAL* 3.3 11.0 - - - +
187B LEU* 1.3 77.1 - - - +
189B LEU* 1.3 57.0 + - - +
191B HIS* 2.9 26.9 + - - +
192B LEU* 4.0 2.8 + - - +
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Residues in contact with LEU 189 (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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2B ILE* 4.0 26.2 - - + +
4B VAL* 3.6 24.7 - - + -
25B LEU* 4.4 6.3 - - + -
29B VAL* 4.1 19.8 - - + +
32B LYS* 5.3 1.4 - - - +
34B LEU* 3.7 29.4 - - + -
62B LEU* 3.7 20.6 - - + -
185B VAL* 2.8 31.6 + - + +
186B ARG* 3.4 13.0 - - - +
188B ALA* 1.3 76.7 - - - +
190B GLU* 1.3 62.0 + - - +
192B LEU* 3.0 26.2 + - + +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.6 12.3 - - + -
30B ASP* 3.4 31.1 - - - +
120B ARG* 4.9 6.9 + - - +
186B ARG* 2.7 47.5 + - - +
187B LEU* 3.4 24.6 - - - +
188B ALA 3.1 0.4 - - - -
189B LEU* 1.3 76.6 - - - +
191B HIS* 1.3 64.6 + - + +
192B LEU* 3.3 6.8 + - - +
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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