Contacts of the helix formed by residues 181 - 187 (chain E) in PDB entry 6A5T
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 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339A LEU* 3.8 20.3 - - - +
1343A GLY* 3.2 18.7 - - - -
1344A ILE* 2.9 33.6 + - - +
1382A GLY* 5.1 1.1 - - - +
177E ILE* 3.7 30.7 - - + +
178E GLN* 3.8 21.6 + - + +
179E ARG 3.2 3.4 - - - -
180E GLU* 1.3 74.1 - - - +
182E PRO* 1.3 55.3 - - - +
183E VAL* 2.4 6.6 + - - +
184E ALA* 2.4 36.2 + - - -
185E ARG 3.4 0.7 + - - -
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Residues in contact with PRO 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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1339A LEU 4.4 1.6 - - - +
1340A SER 3.3 19.7 - - - +
1341A VAL* 3.2 27.4 - - - +
1343A GLY* 4.4 6.7 - - - +
134E PHE* 5.2 0.7 - - - -
143E ILE* 5.2 9.1 - - + +
180E GLU 3.1 11.1 - - - +
181E ASP* 1.3 85.4 - - + +
183E VAL* 1.3 58.1 + - + +
184E ALA 3.3 0.2 - - - -
185E ARG* 3.5 21.9 + - + +
186E TYR* 2.9 28.5 + - - +
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Residues in contact with VAL 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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1343A GLY* 4.6 13.9 - - - -
1344A ILE 5.5 1.1 - - - +
143E ILE* 3.6 26.7 - - + -
144E THR* 4.2 9.0 - - + -
149E VAL* 3.9 18.4 - - + -
152E HIS* 3.2 45.5 - - + +
177E ILE* 5.2 2.9 - - + -
181E ASP* 2.4 15.5 + - - +
182E PRO* 1.3 73.7 - - - +
184E ALA* 1.3 57.1 + - - +
186E TYR* 2.9 21.3 + - + +
187E LEU* 3.1 17.1 + - + +
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Residues in contact with ALA 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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177E ILE* 3.7 13.7 - - + +
178E GLN 3.6 15.3 - - - +
179E ARG* 3.3 20.9 - - - +
181E ASP 2.4 23.8 + - - +
183E VAL* 1.3 70.2 - - - +
185E ARG* 1.3 58.7 + - - +
187E LEU 3.5 0.3 + - - -
188E GLY 3.2 2.8 + - - -
189E LEU* 3.0 56.3 + - + +
213E CYS* 5.1 0.2 - - - -
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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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25E ARG* 4.6 1.4 + - - -
132E GLU* 4.7 1.6 - - - +
133E THR* 4.2 8.5 + - - +
134E PHE* 3.3 64.0 - - + +
135E GLN 3.7 7.7 - - - +
138E ASP* 5.0 13.1 + - - +
179E ARG 4.1 2.2 - - - +
180E GLU* 3.7 46.3 + - + +
181E ASP 3.4 1.8 + - - -
182E PRO* 3.7 19.9 - - - +
183E VAL 3.3 0.2 - - - -
184E ALA* 1.3 71.5 - - - +
186E TYR* 1.3 59.2 + - - +
187E LEU 3.0 4.5 - - - -
188E GLY* 2.8 21.5 + - - +
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Residues in contact with TYR 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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17E THR* 4.3 9.1 + - + -
20E GLU* 4.1 0.3 - - - +
21E MET* 3.5 56.8 + - + +
24E ASP* 2.5 37.3 + - + -
25E ARG* 3.9 5.2 - - - -
134E PHE* 4.2 8.5 - + + -
139E LEU* 4.9 7.2 - - + -
142E ASN* 3.1 33.4 + - - -
143E ILE* 5.4 8.3 - - + -
144E THR* 3.7 24.7 - - + -
182E PRO 2.9 15.6 + - - +
183E VAL* 2.9 15.7 + - + +
185E ARG* 1.3 76.1 - - - +
187E LEU* 1.3 69.5 + - + +
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Residues in contact with LEU 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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24E ASP* 4.5 17.9 - - + +
25E ARG* 3.4 25.3 + - + +
144E THR* 6.2 0.2 - - + -
152E HIS* 3.6 40.8 - - + +
154E ARG* 4.6 27.5 + - + +
183E VAL* 3.1 14.7 + - + +
184E ALA 4.4 2.7 - - - +
185E ARG 3.0 0.6 - - - -
186E TYR* 1.3 105.1 - - + +
188E GLY* 1.3 67.7 + - - +
189E LEU* 4.6 12.2 - - + +
195E VAL* 5.3 7.0 - - + -
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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