Contacts of the helix formed by residues 175 - 184 (chain A) in PDB entry 1EFT
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 ALA 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR* 3.8 11.2 - - + +
27A LEU* 3.8 37.0 - - + +
30A ALA* 3.9 3.7 - - + +
134A PHE* 4.3 5.3 - - + -
136A ASN* 2.9 24.8 + - - +
174A SER* 1.3 72.3 - - - +
176A LEU* 1.3 61.1 + - - +
177A LEU 3.2 0.2 - - - -
178A ALA* 3.8 4.6 - - - +
179A LEU* 2.9 31.4 + - - +
199A ILE* 4.5 6.1 - - - -
406A GNP 3.3 0.2 + - - -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.7 15.1 - - + +
139A ASP* 5.8 0.2 - - - +
174A SER* 3.3 1.0 - - - +
175A ALA* 1.3 80.2 - - - +
177A LEU* 1.3 65.3 + - + +
179A LEU* 3.5 9.5 + - + +
180A GLU* 3.0 27.1 + - + +
406A GNP 3.4 65.5 + - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP* 3.9 20.4 - - + +
174A SER* 3.4 16.0 + - - +
175A ALA 3.2 0.2 - - - -
176A LEU* 1.3 88.0 - - + +
178A ALA* 1.3 65.4 + - - +
179A LEU 3.3 0.4 - - - -
180A GLU* 3.7 19.9 - - + +
181A GLU* 3.2 23.0 + - - +
195A TRP* 3.5 53.4 - - + +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 4.7 3.8 - - + -
34A VAL* 5.1 1.6 - - + -
174A SER 3.4 17.4 + - - +
175A ALA 3.8 3.6 - - - +
177A LEU* 1.3 77.8 - - - +
179A LEU* 1.3 60.5 + - - +
181A GLU* 3.3 4.0 + - - +
182A MET* 3.2 27.8 + - - +
195A TRP* 3.7 20.3 - - - +
196A VAL* 4.0 8.3 - - + +
199A ILE* 3.6 29.8 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 4.0 24.2 - - + +
29A ALA* 4.0 9.4 - - + -
30A ALA* 3.9 22.4 - - + +
33A PHE* 3.8 35.2 - - + -
46A ASP* 4.3 10.3 - - - +
47A TYR* 4.8 9.9 - - + -
175A ALA 2.9 18.5 + - - +
176A LEU* 3.7 12.8 - - + +
178A ALA* 1.3 77.2 - - - +
180A GLU* 1.3 61.9 + - - +
182A MET* 3.4 4.8 + - - +
183A HIS* 2.9 39.7 + - + -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.0 18.5 + - + +
177A LEU* 3.6 21.9 + - + +
178A ALA 3.4 0.4 - - - -
179A LEU* 1.3 75.3 - - - +
181A GLU* 1.3 68.3 + - + +
183A HIS* 3.0 19.6 + - - +
184A LYS* 3.0 47.0 + - + +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 3.2 14.1 + - - +
178A ALA 3.7 4.3 - - - +
179A LEU 3.3 0.2 - - - -
180A GLU* 1.3 84.7 - - + +
182A MET* 1.3 58.5 + - - +
183A HIS 3.0 0.7 - - - -
184A LYS* 4.3 18.3 + - - +
185A ASN* 2.8 34.9 + - - +
188A THR* 3.0 23.7 + - + +
192A GLU* 5.4 1.4 - - - +
193A ASN* 3.5 29.5 + - - +
195A TRP* 6.3 0.2 - - + -
196A VAL* 3.7 23.3 - - + -
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Residues in contact with MET 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 5.1 0.4 - - - +
33A PHE* 3.4 55.4 - - + +
34A VAL* 4.0 14.8 - - + -
37A ALA* 4.1 3.8 - - + -
178A ALA 3.2 16.8 + - - +
179A LEU* 3.8 6.3 - - - +
180A GLU 3.3 0.2 - - - -
181A GLU* 1.3 76.2 - - - +
183A HIS* 1.3 57.7 + - - +
185A ASN 3.5 6.3 - - - +
186A PRO* 3.1 52.2 - - + +
188A THR* 3.7 32.3 - - - +
196A VAL* 3.8 19.5 - - + -
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.9 21.1 - + - -
46A ASP* 2.8 41.0 + - - -
179A LEU* 2.9 36.1 + - + +
180A GLU* 3.0 15.4 + - - +
182A MET* 1.3 79.6 - - - +
184A LYS* 1.3 65.6 + - + +
186A PRO* 4.0 9.4 - - - +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.0 52.0 + - + +
181A GLU* 3.8 19.0 + - - +
183A HIS* 1.3 78.4 - - + +
185A ASN* 1.3 62.1 + - + +
186A PRO* 3.7 4.7 - - - +
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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