Contacts of the helix formed by residues 179 - 188 (chain B) in PDB entry 3E6D
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 SER 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B PRO 3.7 4.8 + - - -
178B LEU* 1.3 77.7 - - - +
180B GLN* 1.3 63.5 + - - +
181B LYS* 3.6 13.8 + - - +
182B SER* 3.1 27.4 + - - -
183B ILE* 3.1 19.6 + - - +
209B LYS* 4.1 4.5 - - - +
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Residues in contact with GLN 180 (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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178B LEU 3.8 0.8 + - - -
179B SER* 1.3 71.5 - - - +
181B LYS* 1.3 61.5 + - - +
183B ILE* 3.5 11.6 + - - +
184B GLY* 3.1 17.7 + - - -
191B HIS* 4.5 5.4 + - - +
194B VAL* 3.8 13.0 - - + +
195B SER* 2.7 41.4 + - - +
198B LEU* 3.9 28.0 - - + +
209B LYS* 4.6 7.1 - - - +
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP* 3.8 23.3 - - - +
71A SER* 5.4 6.3 - - - +
73A LYS* 5.7 2.9 - - - +
155A ARG* 5.3 0.2 - - - +
179B SER* 3.1 12.3 + - - +
180B GLN* 1.3 76.6 - - - +
182B SER* 1.3 66.8 + - - +
184B GLY* 3.1 3.5 + - - -
185B GLU* 2.9 64.3 + - + +
191B HIS* 6.2 4.0 - - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG* 3.3 12.7 + - - +
159A GLU* 3.2 29.7 + - - -
178B LEU* 4.2 9.6 - - - -
179B SER* 3.1 21.6 + - - -
181B LYS* 1.3 81.3 + - - +
183B ILE* 1.3 61.2 + - - +
185B GLU* 3.1 10.4 + - - +
186B ILE* 2.8 37.1 + - - +
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Residues in contact with ILE 183 (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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153B ILE* 4.1 27.1 - - + -
156B LEU* 4.2 13.9 - - + -
157B PHE* 3.8 24.9 - - + -
178B LEU* 3.6 33.4 - - + +
179B SER 3.1 15.5 + - - +
180B GLN* 3.6 12.8 - - - +
182B SER* 1.3 75.1 - - - +
184B GLY* 1.3 55.7 + - - +
186B ILE* 3.5 5.1 + - - -
187B THR* 2.7 36.1 + - - +
194B VAL* 4.1 14.6 - - + -
198B LEU* 4.4 7.9 - - + -
209B LYS* 4.2 9.6 - - + -
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Residues in contact with GLY 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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73A LYS* 6.2 0.2 - - - -
180B GLN 3.1 10.2 + - - -
181B LYS* 3.1 8.1 + - - -
183B ILE* 1.3 77.0 - - - +
185B GLU* 1.3 55.7 + - - +
187B THR* 4.1 1.6 - - - -
188B GLY* 3.0 26.9 + - - -
189B VAL 3.1 27.7 + - - +
191B HIS* 5.7 1.3 - - - -
194B VAL* 4.0 9.1 - - - +
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Residues in contact with GLU 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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71A SER* 5.2 4.7 + - - -
73A LYS* 4.0 31.5 - - - +
151A ILE* 5.4 2.9 - - + +
152A ARG* 3.3 25.3 + - - +
155A ARG* 2.9 43.1 + - + +
181B LYS* 2.9 46.4 + - + +
182B SER* 3.1 9.5 + - - +
184B GLY* 1.3 76.2 - - - +
186B ILE* 1.3 61.5 + - - +
188B GLY* 4.2 0.5 + - - -
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Residues in contact with ILE 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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152A ARG* 3.4 23.4 - - - +
155A ARG* 4.0 9.0 - - + +
156A LEU* 3.8 45.8 - - + +
159A GLU* 3.9 29.2 - - + -
186A ILE* 3.9 24.5 - - + -
187A THR* 3.4 12.7 - - + +
156B LEU* 4.6 9.4 - - + -
178B LEU* 4.6 9.6 - - + -
182B SER 2.8 21.8 + - - +
183B ILE* 4.0 4.9 - - - +
185B GLU* 1.3 78.7 - - - +
187B THR* 1.3 63.8 + - + +
188B GLY 3.4 0.2 - - - -
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Residues in contact with THR 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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186A ILE 3.5 20.2 - - - +
187A THR 3.8 5.4 - - - +
152B ARG* 2.9 56.8 + - - +
153B ILE* 4.1 10.7 - - + +
156B LEU* 4.2 15.5 - - + -
183B ILE* 2.7 23.3 + - + +
186B ILE* 1.3 86.4 - - + +
188B GLY* 1.3 59.9 + - - +
189B VAL* 3.4 21.5 + - - +
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Residues in contact with GLY 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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152A ARG* 3.5 33.4 + - - +
149B PRO* 5.6 0.7 - - - +
152B ARG* 3.6 12.5 + - - -
184B GLY 3.0 8.0 + - - -
185B GLU 4.2 1.0 + - - -
186B ILE 3.4 3.2 - - - -
187B THR* 1.3 78.9 - - - +
189B VAL* 1.3 59.0 + - - +
190B HIS 4.4 0.3 + - - -
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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