Contacts of the helix formed by residues 179 - 193 (chain B) in PDB entry 5ID3
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 GLU 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B ARG* 1.4 89.9 - - + +
180B LYS* 1.4 63.6 + - + +
181B LYS* 3.4 2.6 - - - +
182B LEU* 3.3 38.9 + - - +
183B LEU* 3.0 48.9 + - + +
186B LEU* 5.7 3.5 - - - +
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Residues in contact with LYS 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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171A VAL* 6.1 6.4 - - + +
178B ARG* 4.9 5.3 - - + +
179B GLU* 1.4 78.4 - - + +
181B LYS* 1.4 63.6 + - - +
183B LEU* 3.3 21.2 + - + +
184B LEU* 3.5 22.5 + - + +
314C ARG* 6.4 0.7 - - - +
315C ASP* 3.9 21.7 + - - +
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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
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174B TYR* 5.0 11.4 - - - -
176B LEU 5.1 1.1 - - - +
177B SER* 3.2 40.8 - - - +
178B ARG 5.6 0.8 - - - +
179B GLU 3.4 1.0 - - - +
180B LYS* 1.4 78.9 - - - +
182B LEU* 1.4 62.5 + - - +
184B LEU 3.6 0.5 + - - -
185B GLN* 3.4 44.6 + - - +
311C LYS* 3.6 32.4 - - + +
312C ARG* 5.4 11.4 - - - +
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Residues in contact with LEU 182 (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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170B SER* 5.3 8.5 - - - +
178B ARG 5.8 0.4 - - - +
179B GLU* 3.3 41.1 + - - +
181B LYS* 1.4 82.3 - - - +
183B LEU* 1.4 51.1 + - - +
185B GLN* 3.3 21.9 + - + +
186B LEU* 2.8 41.5 + - + +
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Residues in contact with LEU 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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179B GLU* 3.0 39.3 + - + +
180B LYS* 3.3 16.5 + - + +
182B LEU* 1.4 77.0 - - - +
184B LEU* 1.4 67.5 + - + +
186B LEU* 3.1 30.9 + - + +
187B GLU* 3.2 19.2 + - - +
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Residues in contact with LEU 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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180B LYS* 3.5 15.9 + - + +
181B LYS 3.6 2.7 + - - +
182B LEU 3.5 0.4 - - - -
183B LEU* 1.4 78.8 - - + +
185B GLN* 1.4 62.1 + - - +
187B GLU* 3.2 40.6 + - - +
188B ASN* 3.4 20.5 + - - +
305B GLU* 5.7 0.9 - - + +
308B ASN* 5.3 3.6 - - + +
309B GLN* 3.5 25.1 - - - +
307C ARG* 3.2 28.4 + - - +
311C LYS* 3.8 20.2 - - + -
314C ARG* 3.8 26.9 - - - +
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Residues in contact with GLN 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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181B LYS* 3.4 42.9 + - - +
182B LEU* 3.3 22.1 + - + +
184B LEU* 1.4 75.6 - - - +
186B LEU* 1.4 57.4 + - - +
188B ASN* 3.2 13.6 + - - +
189B ALA* 2.9 27.7 + - - +
308C ASN* 4.2 18.1 - - - +
311C LYS* 3.7 20.8 - - - +
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Residues in contact with LEU 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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179B GLU* 5.7 3.1 - - - +
182B LEU* 2.8 22.7 + - + +
183B LEU* 3.1 30.5 + - + +
185B GLN* 1.4 76.8 - - - +
187B GLU* 1.4 63.8 + - + +
189B ALA* 3.2 11.2 + - + +
190B GLU* 3.2 23.5 + - + +
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Residues in contact with GLU 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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183B LEU* 3.2 12.8 + - - +
184B LEU* 3.2 34.6 + - - +
186B LEU* 1.4 76.8 - - + +
188B ASN* 1.4 65.0 + - - +
190B GLU* 3.4 9.5 + - - +
191B THR* 3.2 24.1 + - - -
305B GLU* 3.8 24.7 - - + +
308B ASN* 6.2 0.3 - - - +
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Residues in contact with ASN 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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184B LEU 3.4 16.2 + - - +
185B GLN* 3.2 14.3 + - - +
187B GLU* 1.4 78.4 - - - +
189B ALA* 1.4 56.9 + - - +
191B THR* 3.3 6.7 + - - -
192B LEU* 3.1 37.5 + - + +
302B GLU* 3.6 36.8 + - - +
305B GLU* 4.2 10.1 - - - +
304C ASP 5.3 0.4 + - - -
307C ARG* 3.7 35.2 + - - +
308C ASN* 4.6 11.5 - - - +
311C LYS* 6.2 0.6 - - - +
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Residues in contact with ALA 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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185B GLN 2.9 12.8 + - - +
186B LEU* 3.2 15.2 + - + +
188B ASN* 1.4 77.0 - - - +
190B GLU* 1.4 51.8 + - - +
192B LEU* 3.4 11.8 + - - +
193B LEU* 2.9 33.3 + - - +
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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
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186B LEU* 3.2 16.0 + - + +
187B GLU* 3.4 10.7 + - - +
189B ALA* 1.4 74.7 - - - +
191B THR* 1.4 72.7 + - - +
193B LEU* 3.2 31.8 - - + +
298B ARG* 5.2 0.2 - - - -
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Residues in contact with THR 191 (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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187B GLU 3.2 12.0 + - - -
188B ASN* 3.3 11.8 + - - -
190B GLU* 1.4 85.1 + - - +
192B LEU* 1.4 58.3 + - - +
193B LEU* 3.5 0.5 - - - +
298B ARG* 2.9 72.9 + - + +
299B LEU* 4.4 4.3 + - + -
301B THR* 4.5 4.7 - - - -
302B GLU* 4.0 24.1 - - + +
305B GLU* 4.9 11.4 + - - -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN* 3.1 28.7 + - + +
189B ALA* 3.6 9.6 - - - +
191B THR* 1.4 77.8 - - - +
193B LEU* 1.4 55.7 + - - +
194B ALA* 2.6 26.0 + - + +
197B HIS* 5.9 0.3 + - - -
298B ARG* 4.0 9.1 + - - +
299B LEU* 3.8 26.5 - - + -
302B GLU* 3.9 15.9 - - - +
301C THR* 4.4 4.9 - - - +
304C ASP* 3.9 10.3 - - + +
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Residues in contact with LEU 193 (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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189B ALA 2.9 16.7 + - - +
190B GLU* 3.2 28.9 - - + +
191B THR 3.5 4.0 - - - +
192B LEU* 1.4 68.5 - - - +
194B ALA* 1.4 63.8 + - - +
195B PRO* 3.3 15.1 - - + -
196B LEU* 3.7 38.5 + - + +
197B HIS* 4.3 4.7 + - - +
290B ASN* 5.7 2.5 - - - +
298B ARG* 3.3 41.7 + - - +
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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