Contacts of the helix formed by residues 166 - 178 (chain B) in PDB entry 1EEJ
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 ASP 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B GLU* 3.9 6.1 + - - +
133B GLU* 5.6 0.9 - - - +
137B LYS* 5.1 0.9 - - - +
164B ASP 3.4 6.1 + - - +
165B VAL* 1.3 78.4 - - - +
167B ILE* 1.3 56.9 + - - +
168B ALA* 3.0 22.8 + - - +
169B ASP* 2.9 39.9 + - - +
170B HIS* 3.7 6.1 - - - -
1001B MES 3.4 23.0 - - - +
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Residues in contact with ILE 167 (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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122B ALA* 3.7 34.3 - - + +
124B PRO* 4.0 15.7 - - + -
128B LEU* 4.7 0.4 - - + -
133B GLU* 3.7 39.1 + - + +
136B MET* 4.2 7.0 - - + +
137B LYS* 3.9 36.6 - - + +
140B TRP* 4.5 3.4 - - + -
165B VAL* 4.0 18.8 - - + -
166B ASP* 1.3 74.0 + - - +
168B ALA* 1.3 62.8 + - - +
170B HIS* 3.0 11.9 + - + +
171B TYR* 2.9 20.6 + - - +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 3.7 35.8 - - + +
133B GLU* 5.2 0.8 + - - -
166B ASP* 3.0 16.8 + - - +
167B ILE* 1.3 79.0 - - - +
169B ASP* 1.3 56.1 + - - +
171B TYR* 3.8 0.9 - - - +
172B ALA* 2.8 33.3 + - - +
1001B MES 3.7 21.5 - - - +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.2 23.0 - - + +
77B GLU* 5.2 2.5 - - - +
166B ASP* 2.9 30.4 + - - +
168B ALA* 1.3 76.0 - - - +
170B HIS* 1.3 60.7 + - - +
172B ALA* 4.0 3.5 - - - +
173B LEU* 2.9 32.4 + - - +
1001B MES 2.6 43.7 + - - +
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.9 19.3 - - + -
77B GLU* 2.8 34.5 + - - +
93B PHE* 3.4 13.9 - - - -
121B LEU* 3.7 21.2 - - + +
122B ALA* 2.9 44.9 + - - +
140B TRP* 3.6 32.5 - + - -
165B VAL* 4.1 7.8 - - + +
166B ASP 3.7 9.4 - - - -
167B ILE* 3.0 10.9 + - + +
169B ASP* 1.3 75.5 - - - +
171B TYR* 1.3 56.3 + - - +
173B LEU* 3.8 0.7 - - - +
174B GLY* 2.9 24.1 + - - -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA 3.6 1.9 + - - -
123B PHE* 3.5 33.2 - + - -
124B PRO* 3.3 41.1 - - + -
125B ARG 4.9 4.3 + - - -
127B GLY* 4.0 16.1 + - - -
128B LEU* 4.1 31.6 - - + -
167B ILE 2.9 15.3 + - - +
168B ALA 3.8 2.9 - - - +
170B HIS* 1.3 76.7 - - - +
172B ALA* 1.3 68.3 + - + +
174B GLY 3.2 2.1 + - - -
175B VAL* 2.9 43.0 + - + +
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Residues in contact with ALA 172 (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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168B ALA 2.8 23.7 + - - +
169B ASP* 4.0 2.5 - - - +
171B TYR* 1.3 78.9 - - + +
173B LEU* 1.3 57.6 + - - +
175B VAL* 3.2 7.3 + - - +
176B GLN* 2.9 37.6 + - + +
1001B MES 3.8 21.3 - - - -
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Residues in contact with LEU 173 (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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31B LEU* 5.8 1.1 - - + -
67B LEU* 3.8 21.5 - - + +
70B GLN* 3.8 23.6 - - + -
71B LEU* 3.6 39.3 - - + +
74B LEU* 3.6 25.6 - - + -
93B PHE* 4.7 3.8 - - + -
169B ASP 2.9 19.6 + - - +
170B HIS* 3.8 3.4 - - - +
172B ALA* 1.3 72.9 - - - +
174B GLY* 1.3 67.3 + - - +
176B GLN* 3.2 5.3 + - + +
177B LEU* 2.9 44.2 + - + +
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Residues in contact with GLY 174 (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 PHE* 3.7 17.4 - - - -
123B PHE* 3.9 4.0 - - - -
170B HIS 2.9 11.3 + - - -
171B TYR 3.6 3.1 - - - -
173B LEU* 1.3 76.8 - - - +
175B VAL* 1.3 61.0 + - - +
177B LEU* 3.1 3.1 + - - +
178B GLY 3.0 5.7 + - - -
179B VAL* 2.8 48.1 + - - +
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Residues in contact with VAL 175 (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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123B PHE* 3.8 14.1 - - + -
171B TYR* 2.9 43.2 + - + +
172B ALA* 3.5 9.0 - - - +
174B GLY* 1.3 76.0 - - - +
176B GLN* 1.3 64.1 + - + +
178B GLY* 3.0 14.0 + - - -
179B VAL 4.5 8.7 - - - +
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Residues in contact with GLN 176 (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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31B LEU* 3.8 18.0 - - + +
32B THR 3.0 26.2 + - - -
33B ASN* 4.2 8.3 + - - +
35B GLY* 3.4 24.2 - - - +
36B VAL* 4.3 0.9 + - - +
67B LEU* 3.8 32.2 - - + +
172B ALA* 2.9 25.0 + - + +
173B LEU* 3.6 9.9 - - + +
175B VAL* 1.3 78.6 - - + +
177B LEU* 1.3 61.0 + - - +
178B GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 177 (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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64B ASN* 6.3 0.2 - - - -
67B LEU* 3.9 30.5 - - + -
68B LEU* 5.0 13.2 - - + -
71B LEU* 5.1 9.9 - - + -
93B PHE* 4.0 25.1 - - + -
173B LEU* 2.9 38.3 + - + +
174B GLY* 3.6 5.2 - - - +
176B GLN* 1.3 76.9 - - - +
178B GLY* 1.3 58.5 + - - +
179B VAL* 4.8 1.3 - - + -
186B VAL* 4.3 13.7 - - + -
190B GLY 5.4 5.8 - - - +
192B LEU* 3.4 24.4 - - + +
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Residues in contact with GLY 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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175B VAL 3.0 12.3 + - - -
176B GLN 3.3 1.0 + - - -
177B LEU* 1.3 78.8 - - - +
179B VAL* 1.3 66.9 + - - +
180B SER* 3.2 9.9 + - - -
192B LEU* 3.4 13.3 - - - +
194B PRO* 5.0 3.3 - - - +
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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