Contacts of the helix formed by residues 179 - 193 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E LYS* 5.0 22.4 - - + +
177E SER* 5.9 0.9 - - - -
178E ARG* 1.4 77.1 - - - +
180E LYS* 1.4 84.4 + - + +
181E LYS 3.3 2.2 - - - -
182E LEU* 3.3 11.8 + - + +
183E LEU* 3.0 40.4 + - - +
186E LEU* 5.3 4.5 - - - +
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Residues in contact with LYS 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ARG* 3.9 17.7 - - - +
171D VAL* 4.6 25.3 - - - +
177E SER* 5.8 4.7 - - - +
178E ARG* 4.7 3.3 - - - +
179E GLU* 1.4 95.4 + - + +
181E LYS* 1.4 63.5 + - + +
183E LEU* 3.2 24.2 + - + +
184E LEU* 3.4 16.4 + - + +
312E ARG* 5.0 8.5 - - - +
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Residues in contact with LYS 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 3.6 42.8 - - + +
312A ARG* 4.3 7.2 - - - +
314A ARG* 4.9 7.2 - - - +
315A ASP* 3.4 45.3 + - + +
318B GLU* 4.2 19.5 + - - -
178E ARG* 5.4 15.2 - - + +
179E GLU* 3.3 0.6 - - - +
180E LYS* 1.4 76.5 - - + +
182E LEU* 1.4 73.3 + - + +
184E LEU* 3.4 7.8 + - - +
185E GLN* 3.4 25.3 + - - +
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Residues in contact with LEU 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ARG* 3.3 26.7 - - + +
179E GLU* 3.3 14.3 + - + +
181E LYS* 1.4 85.1 - - + +
183E LEU* 1.4 60.0 + - - +
185E GLN* 3.2 13.3 + - + +
186E LEU* 2.9 45.0 + - + +
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Residues in contact with LEU 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA 5.5 6.3 - - - +
171D VAL* 5.6 12.3 - - + -
179E GLU* 3.0 34.8 + - - +
180E LYS* 3.2 17.5 + - + +
182E LEU* 1.4 74.9 - - - +
184E LEU* 1.4 65.5 + - + +
186E LEU* 3.4 11.3 + - + +
187E GLU* 3.0 42.4 + - + +
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Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ARG* 2.7 40.5 + - - +
311A LYS* 4.4 7.0 - - + -
314A ARG* 3.4 32.1 - - - +
180E LYS* 3.4 13.3 + - - +
181E LYS 3.8 7.9 - - - +
182E LEU 3.4 0.6 - - - -
183E LEU* 1.4 84.6 - - + +
185E GLN* 1.4 57.3 + - - +
187E GLU* 3.3 18.3 + - + +
188E ASN 3.4 5.0 + - - -
305E GLU* 4.9 7.4 - - + +
308E ASN* 5.6 4.0 - - + -
309E GLN* 4.1 37.0 - - + +
312E ARG* 5.5 0.7 - - - +
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Residues in contact with GLN 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ARG* 3.0 19.3 + - - +
308A ASN* 2.7 46.7 + - - +
311A LYS* 3.6 18.8 - - - +
181E LYS 3.4 15.4 + - - +
182E LEU* 3.2 16.2 + - + +
184E LEU* 1.4 76.6 - - - +
186E LEU* 1.4 63.9 + - + +
188E ASN* 3.5 5.0 + - - +
189E ALA* 3.3 20.5 + - - +
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Residues in contact with LEU 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E GLU* 5.3 4.5 - - - +
182E LEU* 2.9 32.6 + - + +
183E LEU* 3.6 11.9 - - + +
185E GLN* 1.4 75.5 - - + +
187E GLU* 1.4 58.3 + - - +
189E ALA* 3.2 10.7 + - + +
190E GLU* 3.0 29.1 + - - +
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Residues in contact with GLU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E LEU* 3.0 27.5 + - + +
184E LEU* 3.3 17.2 + - + +
186E LEU* 1.4 74.1 - - - +
188E ASN* 1.4 62.0 + - - +
190E GLU* 3.3 17.7 + - - +
191E THR* 3.2 25.9 + - - +
305E GLU* 3.8 27.4 - - + -
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Residues in contact with ASN 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASP* 3.6 41.5 + - - +
307A ARG* 3.5 31.1 - - + +
308A ASN* 5.3 3.8 - - - +
184E LEU 3.4 3.0 + - - -
185E GLN* 3.7 6.3 + - - +
186E LEU 3.4 0.2 - - - -
187E GLU* 1.4 76.8 - - - +
189E ALA* 1.4 64.9 + - - +
191E THR* 3.3 9.5 + - - -
192E LEU* 3.2 37.4 + - - +
302E GLU* 3.8 17.3 - - - +
305E GLU* 5.2 5.0 - - - +
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Residues in contact with ALA 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E GLN 3.3 10.9 + - - +
186E LEU* 3.2 17.7 + - + +
188E ASN* 1.4 82.4 - - - +
190E GLU* 1.4 61.6 + - - +
192E LEU* 3.3 10.8 + - - +
193E LEU* 3.2 19.4 + - - -
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Residues in contact with GLU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E LEU 3.0 12.4 + - - +
187E GLU* 3.3 22.2 + - - +
189E ALA* 1.4 74.2 - - - +
191E THR* 1.4 62.2 + - - +
193E LEU* 3.5 25.8 - - - +
196E LEU* 4.3 19.1 - - - +
284E ARG* 5.7 0.5 + - - -
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLU* 3.2 13.5 + - - +
188E ASN* 3.3 8.7 + - - -
190E GLU* 1.4 77.3 - - - +
192E LEU* 1.4 62.3 + - - +
193E LEU* 3.3 15.7 - - - +
298E ARG* 2.9 49.9 - - + +
299E LEU* 4.4 1.6 + - - -
301E THR* 4.3 6.3 - - - -
302E GLU* 3.7 23.8 - - + +
305E GLU* 3.5 15.0 + - - +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 5.8 4.0 - - - +
301A THR* 4.3 20.4 - - + -
304A ASP* 5.0 4.3 - - + +
188E ASN* 3.2 26.0 + - - +
189E ALA* 3.3 13.0 + - - +
191E THR* 1.4 77.5 - - - +
193E LEU* 1.4 71.5 + - - +
194E ALA* 4.7 1.4 - - + +
197E HIS* 5.4 0.9 + - - -
299E LEU* 4.6 10.8 - - + -
302E GLU* 2.9 29.4 - - + +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ALA 3.2 11.8 + - - -
190E GLU* 3.5 18.4 - - - +
191E THR* 3.3 20.2 - - - +
192E LEU* 1.4 84.8 - - - +
194E ALA* 1.4 58.3 + - - +
195E PRO* 4.0 3.6 - - - -
196E LEU* 4.3 29.4 - - + -
197E HIS* 3.5 32.9 + - + +
200E LYS* 5.4 3.1 - - + -
288E LYS* 6.0 0.4 - - - +
294E GLU* 4.8 16.6 - - + +
298E ARG* 3.5 33.0 - - + +
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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