Contacts of the helix formed by residues 169 - 180 (chain B) in PDB entry 4FE1
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 ASN 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B SER 3.4 10.6 + - - +
166B TRP* 3.5 20.8 - - + +
167B PHE 3.3 4.3 - - - +
168B LYS* 1.3 72.6 - - - +
170B ALA* 1.3 62.0 + - - +
171B GLU* 3.9 8.5 + - - +
172B SER* 3.3 30.4 + - - -
173B ARG* 3.6 16.9 + - - +
292B THR* 5.6 4.1 - - - +
293B GLN* 4.9 11.7 - - - +
326B TYR* 5.8 0.2 - - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LYS 2.8 7.8 + - - -
169B ASN* 1.3 69.8 - - - +
171B GLU* 1.3 77.0 + - - +
173B ARG* 3.0 15.8 + - - +
174B LEU* 2.9 33.9 + - + +
300B ILE* 5.1 6.3 - - + -
326B TYR* 4.1 12.8 + - + +
329B TYR* 6.6 0.2 - - + -
330B ASN* 3.8 19.1 - - + +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 4.3 7.2 - - - +
170B ALA* 1.3 81.0 + - - +
172B SER* 1.3 61.7 + - - +
174B LEU* 3.4 7.8 + - - +
175B ASN* 3.0 30.0 + - - +
290B TYR* 3.8 15.9 - - + -
291B ARG 3.3 27.4 - - - +
292B THR* 4.0 2.9 - - + -
298B HIS 4.2 0.6 - - - +
299B SER* 4.0 6.2 - - - -
300B ILE* 3.3 37.0 + - - +
326B TYR* 2.6 31.3 + - - -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 3.3 30.5 + - - -
170B ALA 3.3 0.6 - - - -
171B GLU* 1.3 77.8 - - - +
173B ARG* 1.3 57.7 + - - +
175B ASN* 3.8 0.3 - - - +
176B HIS* 3.0 52.8 + - - +
292B THR* 3.6 21.3 - - - +
293B GLN* 5.0 7.4 + - - -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TRP* 6.6 0.4 - - - -
167B PHE* 4.3 19.0 + - - +
169B ASN 3.6 11.8 + - - +
170B ALA* 3.0 15.5 + - - +
172B SER* 1.3 77.5 - - - +
174B LEU* 1.3 61.4 + - + +
176B HIS* 3.4 2.8 + - - -
177B HIS* 2.9 66.6 + - + +
329B TYR* 5.7 4.6 - - - -
330B ASN* 5.5 4.8 + - - -
336B GLN* 4.3 19.0 + - - -
340B HIS* 4.8 14.5 - - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ALA* 2.9 19.5 + - + +
171B GLU* 3.8 6.5 - - - +
173B ARG* 1.3 76.9 - - + +
175B ASN* 1.3 64.0 + - - +
177B HIS* 4.1 2.6 - - + +
178B LEU* 2.9 43.1 + - + +
290B TYR* 3.6 29.4 - - + +
300B ILE* 3.5 32.3 - - + -
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLU 3.0 17.0 + - - +
172B SER 3.8 3.8 - - - +
174B LEU* 1.3 75.5 - - - +
176B HIS* 1.3 62.4 + - + +
178B LEU* 5.1 0.4 - - - -
179B ALA* 3.0 29.1 + - - +
286B ALA 4.5 0.3 - - - +
287B GLY* 3.2 33.7 + - - +
288B HIS* 4.3 2.6 - - - +
289B MET 3.9 3.1 + - - +
290B TYR* 2.9 58.3 + - - +
292B THR* 4.0 11.3 + - + +
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Residues in contact with HIS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B SER* 3.0 42.5 + - - +
173B ARG* 4.1 3.1 - - - +
175B ASN* 1.3 82.0 - - + +
177B HIS* 1.3 65.9 + - + +
179B ALA* 5.2 0.7 - - - -
180B GLY* 2.9 26.0 + - - +
181B LEU* 3.2 6.9 + - - +
292B THR* 6.0 2.2 - - + -
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 2.9 49.1 + - + +
174B LEU* 4.1 3.4 - - + +
176B HIS* 1.3 82.8 - - + +
178B LEU* 1.3 64.5 + - + +
181B LEU* 3.2 34.4 + - + +
182B PHE* 2.8 38.6 + - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LEU* 2.9 35.5 + - + +
175B ASN* 5.1 0.2 - - - -
177B HIS* 1.3 79.7 - - + +
179B ALA* 1.3 58.3 + - - +
182B PHE* 3.3 22.9 - - + +
183B GLY 2.9 22.3 + - - -
283B PHE* 3.1 26.4 - - + +
286B ALA* 3.9 27.1 - - + +
287B GLY* 4.0 12.1 - - - +
289B MET* 6.1 0.9 - - - -
290B TYR* 4.6 14.1 - - + -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASN 3.0 11.3 + - - +
176B HIS* 5.2 0.9 - - - -
178B LEU* 1.3 78.0 - - - +
180B GLY* 1.3 59.2 + - - +
183B GLY* 3.1 3.1 - - - -
184B VAL* 2.9 29.3 + - - +
283B PHE 3.4 7.2 + - - -
284B ILE* 3.8 25.5 - - + +
287B GLY* 3.5 23.6 - - - +
288B HIS* 4.8 4.0 - - + +
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B HIS* 2.9 20.6 + - - +
179B ALA* 1.3 72.1 - - - +
181B LEU* 1.3 65.9 + - - +
182B PHE 3.1 1.9 + - - -
184B VAL* 3.2 29.9 + - - +
185B SER* 3.4 7.1 + - - -
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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