Contacts of the helix formed by residues 170 - 178 (chain E) in PDB entry 5X6E
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 THR 170 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E ASN* 3.3 17.4 + - - -
169E LEU* 1.3 77.0 - - - +
171E MET* 1.3 65.4 + - - +
172E GLN* 3.0 24.5 + - + -
173E GLU* 3.3 29.0 + - - +
174E LEU* 3.3 14.6 + - - +
7H C 4.0 35.7 + - + +
8H A 3.6 17.0 - - - +
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Residues in contact with MET 171 (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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169E LEU 3.8 0.4 + - - -
170E THR* 1.3 74.3 - - - +
172E GLN* 1.3 62.9 + - - +
174E LEU* 3.6 12.1 + - + +
175E GLY 3.5 12.5 + - - -
183E SER* 4.1 20.0 - - - +
186E VAL* 3.8 10.0 - - + +
187E SER* 4.1 15.3 - - - -
190E ILE* 3.5 35.2 - - + -
201E TYR* 5.5 2.0 - - + -
206E PHE* 4.0 27.8 - - + -
8H A 3.1 40.6 + - + +
9H T 3.3 29.8 - - + +
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Residues in contact with GLN 172 (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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170E THR* 3.6 17.2 - - + +
171E MET* 1.3 82.2 - - - +
173E GLU* 1.3 55.8 + - - +
175E GLY* 2.9 18.7 + - - -
176E TYR* 2.8 58.3 + - - -
180E ILE 4.8 0.5 - - - +
181E ALA 5.5 5.9 - - - +
183E SER* 4.0 28.7 - - - +
186E VAL* 5.4 0.2 - - - -
7H C 5.0 9.8 + - - +
8H A 5.2 0.4 - - - +
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Residues in contact with GLU 173 (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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47E LYS* 3.7 29.5 + - - +
59E ASN* 4.0 2.6 + - - +
62E TYR* 2.8 28.4 + - - +
88E ILE* 4.4 8.2 - - - +
168E ASN* 4.0 20.5 + - - +
169E LEU* 4.7 6.6 - - + +
170E THR* 3.3 26.6 + - - +
172E GLN* 1.3 76.0 - - - +
174E LEU* 1.3 59.2 + - - +
175E GLY 3.2 0.2 - - - -
176E TYR* 3.2 21.1 + - + +
177E SER* 2.8 32.8 + - - -
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Residues in contact with LEU 174 (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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143E ILE* 4.6 10.9 - - + +
146E GLN* 5.1 7.4 - - + +
147E LEU* 4.9 14.8 - - + -
150E LEU* 4.4 13.0 - - + -
169E LEU* 3.9 32.5 - - + -
170E THR 3.3 11.8 + - - +
171E MET* 3.6 12.6 - - - +
172E GLN 3.3 0.6 - - - -
173E GLU* 1.3 75.5 - - - +
175E GLY* 1.3 54.8 + - - +
177E SER* 3.2 7.9 + - - +
178E SER* 2.7 37.7 + - - -
186E VAL* 4.2 8.7 - - + -
190E ILE* 4.5 20.6 - - + -
206E PHE* 4.3 24.5 - - + -
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Residues in contact with GLY 175 (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 3.5 4.2 + - - -
172E GLN 2.9 10.3 + - - -
174E LEU* 1.3 79.4 - - - +
176E TYR* 1.3 55.7 + - - +
178E SER* 3.0 19.6 - - - +
179E GLY 3.7 0.5 - - - -
180E ILE* 2.8 51.1 + - - +
181E ALA 5.9 0.2 - - - -
186E VAL* 4.1 9.5 - - - +
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Residues in contact with TYR 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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47E LYS* 5.4 2.2 - - - -
56E THR* 5.9 0.2 - - - -
57E ILE* 3.2 60.9 + - + +
58E MET* 3.7 2.5 - - - +
59E ASN* 2.8 43.2 + - - +
172E GLN* 2.8 40.3 + - - -
173E GLU* 3.4 27.8 - - + +
174E LEU 3.2 0.4 - - - -
175E GLY* 1.3 77.7 - - - +
177E SER* 1.3 61.1 + - - +
178E SER 2.8 13.0 - - - +
180E ILE 4.4 3.6 - - - -
181E ALA* 4.7 15.2 + - - -
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Residues in contact with SER 177 (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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59E ASN* 3.5 20.1 - - - +
62E TYR* 3.5 28.7 + - - -
130E LYS* 4.8 1.0 - - - -
134E PHE* 4.0 9.5 - - - -
146E GLN* 3.5 42.1 - - - +
173E GLU 2.8 19.9 + - - -
174E LEU* 3.6 9.3 - - - +
176E TYR* 1.3 76.3 - - - +
178E SER* 1.3 59.1 + - - +
131F PHE* 4.5 6.1 - - - -
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Residues in contact with SER 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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58E MET* 3.4 14.5 - - - +
134E PHE* 4.3 11.7 - - - -
142E SER* 4.0 21.5 - - - -
143E ILE* 3.7 16.6 - - - +
146E GLN* 5.3 1.5 - - - +
174E LEU 2.7 22.0 + - - -
175E GLY* 3.0 11.4 + - - +
176E TYR 2.8 17.0 - - - +
177E SER* 1.3 76.3 - - - +
179E GLY* 1.3 60.3 + - - +
180E ILE* 3.3 20.0 - - - +
135F SER* 5.0 0.7 - - - -
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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