Contacts of the helix formed by residues 180 - 189 (chain E) in PDB entry 3TMP
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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E SEP 3.0 10.1 + - - +
179E ASP* 1.3 82.5 - - - +
181E TYR* 1.3 65.3 + - + +
182E GLU 3.6 0.4 - - - -
183E ALA* 4.2 2.9 - - - -
184E ALA* 3.3 29.5 + - + +
187E ARG* 5.4 3.9 + - - +
281E ASN* 2.8 26.1 + - - +
329E TYR* 5.0 0.2 + - - -
42F ARG* 2.9 30.6 + - - +
71F LEU 4.4 0.2 - - - +
72F ARG* 3.3 31.0 - - + +
73F LEU 3.2 5.5 + - - -
74F ARG* 3.0 37.7 + - + +
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Residues in contact with TYR 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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171E MET* 3.9 23.0 - - + +
172E GLY* 3.7 23.1 - - - -
175E TYR* 3.5 23.5 - + - -
177E SEP 2.7 61.0 + - - -
178E GLU* 3.2 15.4 + - - +
179E ASP 3.6 0.2 - - - -
180E GLU* 1.3 79.2 - - - +
182E GLU* 1.3 63.2 + - - +
184E ALA* 4.4 1.4 - - - +
185E ALA* 3.6 17.3 + - - +
272E ARG* 3.6 3.8 + - - -
278E CYS* 5.6 0.5 - - - -
74F ARG* 3.4 47.2 + - - +
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Residues in contact with GLU 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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168E GLY* 3.7 11.1 - - - -
169E SER* 2.8 37.6 + - - +
170E HIS 4.6 1.2 + - - -
171E MET* 2.7 27.0 + - + +
178E GLU 4.7 1.6 + - - -
179E ASP 5.2 0.8 + - - -
181E TYR* 1.3 79.3 - - - +
183E ALA* 1.3 58.5 + - - +
185E ALA* 3.3 4.6 + - - +
186E ALA* 2.9 29.3 + - + +
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Residues in contact with ALA 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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179E ASP 4.4 14.5 + - - +
180E GLU 3.8 2.7 + - - +
181E TYR 3.4 0.6 - - - -
182E GLU* 1.3 76.9 - - - +
184E ALA* 1.3 60.7 + - - +
186E ALA* 3.7 7.6 - - - +
187E ARG* 3.0 53.9 + - - +
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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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180E GLU* 3.3 21.8 + - + +
181E TYR 4.4 1.3 - - - +
183E ALA* 1.3 78.3 - - - +
185E ALA* 1.3 62.9 + - - +
187E ARG* 3.6 25.6 + - - +
188E ILE* 4.0 8.8 + - - +
331E ARG 4.9 1.9 - - - +
332E ASN* 4.1 15.5 - - - +
333E ILE* 4.0 30.4 - - + +
74F ARG* 6.1 1.3 - - + +
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Residues in contact with ALA 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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171E MET* 5.5 7.0 - - + -
181E TYR 3.6 11.5 + - - +
182E GLU* 3.3 10.4 + - - +
184E ALA* 1.3 81.5 - - - +
186E ALA* 1.3 53.1 + - - +
187E ARG 3.5 0.3 + - - -
188E ILE* 3.9 4.3 + - - +
189E GLU* 2.6 43.0 + - - +
333E ILE* 5.1 2.0 - - - +
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Residues in contact with ALA 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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182E GLU* 2.9 20.8 + - + +
183E ALA* 4.0 7.9 - - - +
185E ALA* 1.3 74.1 - - - +
187E ARG* 1.3 70.1 + - - +
188E ILE 3.4 0.2 + - - -
189E GLU* 2.5 23.2 + - - +
190E ALA* 4.1 4.7 + - - +
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Residues in contact with ARG 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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180E GLU* 5.4 3.8 + - - +
183E ALA* 3.0 48.2 + - - +
184E ALA* 3.7 12.4 - - - +
185E ALA 3.4 0.4 - - - -
186E ALA* 1.3 80.5 - - - +
188E ILE* 1.3 63.3 + - + +
189E GLU 3.1 3.3 + - - -
190E ALA* 3.2 19.4 + - - +
191E MET* 4.7 1.4 + - - +
331E ARG 5.7 0.2 - - - +
332E ASN* 2.5 37.1 + - + -
39F ASP* 4.6 24.6 + - - +
72F ARG* 5.3 10.1 - - - +
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Residues in contact with ILE 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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184E ALA 4.0 10.5 + - - +
185E ALA* 3.9 4.9 + - - +
186E ALA 3.5 0.6 - - - -
187E ARG* 1.3 75.9 - - + +
189E GLU* 1.3 64.1 + - + +
190E ALA 3.0 6.3 + - - -
191E MET* 3.5 40.8 + - - +
196E VAL* 3.9 17.2 - - + +
331E ARG* 3.9 49.4 - - + +
333E ILE* 5.0 10.3 - - + -
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Residues in contact with GLU 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 ALA* 2.6 30.5 - - + +
186E ALA* 2.5 34.1 - - - +
187E ARG 3.1 0.2 + - - -
188E ILE* 1.3 81.9 - - + +
190E ALA* 1.3 58.7 + - - +
191E MET 3.5 3.4 + - - +
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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