Contacts of the helix formed by residues 175 - 185 (chain E) in PDB entry 5ITX
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 GLY 175 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E GLU* 1.3 63.9 + - - +
54E LYS* 3.2 2.7 - - - -
166E LEU* 3.4 9.8 - - - +
173E GLY 3.5 0.6 + - - -
174E ILE* 1.3 73.6 - - - +
176E ASN* 1.3 56.5 + - - -
178E LEU* 3.2 2.1 + - - +
179E ARG* 2.9 30.0 + - - +
298F G 2.8 11.2 - - - -
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Residues in contact with ASN 176 (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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3E GLU* 2.5 2.4 + - - -
166E LEU* 3.7 2.8 - - + +
175E GLY* 1.3 70.1 - - - -
177E TYR* 1.3 61.3 + - - +
179E ARG* 2.6 60.2 + - - +
180E ALA* 3.7 8.8 + - - +
263E TYR* 3.7 8.6 + - - -
277E ARG* 3.5 33.8 - - - +
278E THR* 3.0 21.9 + - - +
279E ILE* 5.2 0.2 - - - +
280E TRP* 5.7 0.2 - - - -
297F CTG 2.9 33.5 + - - +
298F G 2.8 8.3 + - - +
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Residues in contact with TYR 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E GLU* 2.8 27.7 + - + -
5E PRO* 3.4 22.9 - - - +
6E GLU* 2.9 28.6 + - - -
176E ASN* 1.3 76.8 - - - +
178E LEU* 1.3 89.7 + - + +
180E ALA* 3.4 3.1 + - - +
181E GLU* 3.2 25.8 + - - +
236E VAL* 3.6 7.7 - - + +
256E PHE* 3.7 29.6 - + + -
259E TRP* 3.9 16.6 - + - -
260E LEU* 4.3 2.5 - - + -
263E TYR* 3.4 38.7 - - + +
297F CTG 3.8 25.4 + - + +
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Residues in contact with LEU 178 (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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3E GLU* 3.3 6.9 + - + +
5E PRO* 3.6 27.1 - - + -
173E GLY 3.9 17.9 - - - +
174E ILE* 4.3 17.0 - - + -
175E GLY 3.2 10.1 + - - +
177E TYR* 1.3 108.8 - - + +
179E ARG* 1.3 65.2 + - - +
181E GLU* 3.4 2.5 + - - +
182E ILE* 3.0 31.2 + - + +
232E VAL* 4.0 17.5 - - + -
233E PRO* 3.9 31.6 - - + -
236E VAL* 4.4 0.4 - - + -
259E TRP* 4.4 4.5 - - + -
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Residues in contact with ARG 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E CYS* 2.8 43.6 + - - -
163E GLU* 4.1 0.4 - - - +
165E LEU* 4.1 27.1 - - + -
166E LEU* 3.5 24.4 - - + +
174E ILE* 4.4 6.4 - - + +
175E GLY 2.9 12.3 + - - +
176E ASN* 2.6 35.9 + - - +
178E LEU* 1.3 77.0 - - - +
180E ALA* 1.3 67.3 + - - +
182E ILE* 3.7 2.9 - - - +
183E LEU* 3.0 31.3 + - + +
273E ASP* 2.8 28.6 + - - -
277E ARG* 3.2 21.8 + - - +
278E THR 3.2 10.1 + - - -
279E ILE* 3.4 24.3 - - + +
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Residues in contact with ALA 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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176E ASN 3.9 9.4 - - - +
177E TYR 3.4 9.1 + - - +
178E LEU 3.2 0.2 - - - -
179E ARG* 1.3 84.9 - - - +
181E GLU* 1.3 58.6 + - - +
183E LEU* 3.9 2.1 - - - +
184E TYR* 3.0 33.7 + - - +
262E CYS* 4.5 2.9 - - - -
263E TYR* 4.3 13.0 - - + -
279E ILE* 4.4 3.4 - - + -
280E TRP* 3.5 42.5 - - + +
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Residues in contact with GLU 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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177E TYR 3.2 16.5 + - - +
178E LEU* 3.8 5.6 - - - +
180E ALA* 1.3 81.0 - - + +
182E ILE* 1.3 62.5 + - - +
184E TYR* 4.1 5.5 - - - +
185E ARG* 3.5 31.5 + - - +
232E VAL* 4.5 7.2 - - + -
259E TRP* 3.8 32.1 - - + -
260E LEU* 3.8 16.5 - - + +
261E ARG* 3.0 32.1 + - - +
262E CYS* 2.8 33.9 + - - +
263E TYR* 3.3 7.6 + - + -
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Residues in contact with ILE 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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165E LEU* 4.9 5.6 - - + -
174E ILE* 3.9 19.3 - - + -
178E LEU* 3.0 24.0 + - + +
179E ARG* 3.7 6.7 - - - +
181E GLU* 1.3 74.5 - - - +
183E LEU* 1.3 70.0 + - - +
185E ARG* 3.1 17.7 + - - +
186E LEU* 3.7 3.5 + - - +
225E LEU* 3.3 32.8 - - + +
228E LEU* 3.8 22.7 - - + +
229E CYS* 3.6 32.1 - - - -
232E VAL* 4.1 26.0 - - + -
233E PRO* 4.9 0.9 - - + -
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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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161E ILE* 3.9 24.9 - - + -
162E CYS* 3.7 32.1 - - + -
165E LEU* 3.8 19.7 - - + -
179E ARG 3.0 16.9 + - - +
180E ALA* 3.9 3.4 - - - +
182E ILE* 1.3 79.1 - - - +
184E TYR* 1.3 55.1 + - - +
186E LEU* 2.8 26.7 + - - +
187E LYS 3.2 7.8 + - - -
188E ILE* 3.4 39.7 + - + +
190E PRO* 4.0 15.0 - - + -
225E LEU* 4.8 4.3 - - + -
279E ILE* 4.3 9.2 - - + -
280E TRP 5.4 2.2 - - - +
281E PHE* 5.9 2.5 - - + -
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Residues in contact with TYR 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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20B ALA* 4.1 22.9 + - - +
180E ALA 3.0 19.1 + - - +
181E GLU 4.1 6.1 - - - +
182E ILE 3.3 0.2 - - - -
183E LEU* 1.3 75.8 - - - +
185E ARG* 1.3 61.1 + - + +
186E LEU 3.2 3.8 + - - -
187E LYS* 3.3 47.3 + - + +
261E ARG* 3.0 46.5 + - + -
262E CYS* 3.8 22.9 - - + -
268E MET* 3.4 21.6 - - + +
280E TRP 5.6 0.2 + - - -
281E PHE* 5.3 5.7 - - - +
282E GLN* 4.0 21.4 + - + +
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Residues in contact with ARG 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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106B PRO* 3.4 43.7 - - + +
107B GLY* 5.1 0.7 - - - -
181E GLU* 3.5 19.9 + - - +
182E ILE 3.1 11.6 + - - +
183E LEU 3.1 0.6 + - - -
184E TYR* 1.3 79.1 - - + +
186E LEU* 1.3 59.0 + - - +
187E LYS* 5.7 0.4 - - - -
228E LEU* 3.9 15.3 - - + +
231E SER* 5.7 0.4 + - - -
232E VAL* 3.9 22.3 - - - +
235E GLU* 2.6 42.4 + - - -
259E TRP* 3.8 20.6 - - - +
261E ARG* 3.5 54.5 - - - +
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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