Contacts of the helix formed by residues 174 - 184 (chain A) in PDB entry 1F89
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 PHE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A HIS* 3.5 46.2 - + + +
170A TYR* 3.3 59.5 - + - -
171A ASP 3.3 12.8 + - - +
172A MET 3.1 1.0 - - - -
173A ARG* 1.3 89.6 - - + +
175A PRO* 1.3 68.2 - - + +
176A GLU* 3.1 6.8 + - - +
177A LEU* 3.3 13.6 + - + +
178A ALA 4.2 1.2 + - - -
191A TYR* 4.8 1.0 + - - -
211A ARG* 4.1 4.5 + - - -
574B VAL* 6.2 0.7 - - + -
575B PRO 4.4 8.3 - - - -
576B LEU* 4.6 1.1 - - - -
577B THR 4.3 5.8 - - - -
578B LYS* 3.3 48.5 - - + -
582B PHE* 4.9 1.8 - + + -
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Residues in contact with PRO 175 (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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173A ARG 3.7 4.5 - - - +
174A PHE* 1.3 78.9 - - - +
176A GLU* 1.3 77.9 + - - +
177A LEU 3.2 0.2 - - - -
178A ALA* 3.0 3.4 + - - +
179A MET* 2.9 44.9 + - + +
211A ARG* 3.3 33.8 - - - +
214A ASP* 5.8 2.2 - - - +
215A ASN* 6.2 0.2 - - - +
475B PRO* 5.8 3.6 - - + -
479B MET* 4.6 13.5 - - + -
483B ARG* 5.1 2.0 - - - +
514B ASP* 3.6 25.6 - - + +
578B LYS* 5.3 7.0 - - - +
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Residues in contact with GLU 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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174A PHE* 3.1 4.7 + - - +
175A PRO* 1.3 90.6 - - - +
177A LEU* 1.3 57.8 + - - +
179A MET* 3.3 17.1 + - + +
180A LEU* 2.9 38.6 + - + +
479B MET* 4.2 2.9 - - - +
483B ARG* 3.0 39.1 + - - -
578B LYS* 5.0 3.5 - - - +
580B ARG* 4.8 4.8 + - - +
582B PHE* 3.4 48.3 - - + -
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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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126A HIS* 5.0 8.1 - - + -
129A VAL* 4.8 11.9 - - + -
130A HIS* 3.4 24.5 - - + +
154A SER* 4.4 13.9 + - - +
167A GLY* 5.0 3.6 - - - -
171A ASP* 3.3 52.0 - - + +
174A PHE 3.3 9.1 + - - +
175A PRO 3.2 0.6 - - - -
176A GLU* 1.3 74.9 - - - +
178A ALA* 1.3 60.8 + - - +
180A LEU* 3.7 5.9 - - + +
181A SER* 3.4 25.6 + - - -
189A MET* 3.9 14.4 - - + +
191A TYR* 4.7 0.9 - - + +
582B PHE* 3.6 22.9 - - + -
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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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174A PHE 4.2 0.4 + - - -
175A PRO 3.0 8.0 + - - +
177A LEU* 1.3 77.1 - - - +
179A MET* 1.3 67.7 + - - +
180A LEU 3.1 1.5 + - - -
181A SER* 3.3 1.2 + - - -
182A ALA* 2.8 27.5 + - - +
189A MET* 4.0 19.4 - - + +
191A TYR* 3.8 9.6 + - - +
211A ARG* 3.7 26.0 - - + +
215A ASN* 3.4 20.4 - - - +
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Residues in contact with MET 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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175A PRO* 2.9 55.3 + - + +
176A GLU* 3.4 16.4 - - + +
178A ALA* 1.3 75.7 - - - +
180A LEU* 1.3 58.1 + - + +
183A ARG* 2.8 76.8 + - - +
214A ASP* 6.3 1.6 - - + -
215A ASN* 2.9 20.8 - - - +
475B PRO* 4.4 7.9 - - + -
476B GLU* 4.3 2.9 - - - +
479B MET* 3.7 29.2 - - + -
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Residues in contact with LEU 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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154A SER* 3.6 25.6 - - - +
176A GLU* 2.9 22.4 + - + +
177A LEU* 3.7 6.3 - - + +
179A MET* 1.3 81.9 - - + +
181A SER* 1.3 63.5 + - - +
183A ARG* 4.1 2.1 - - - +
184A LYS* 3.2 47.5 + - - +
582B PHE* 3.7 36.8 - - + +
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Residues in contact with SER 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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154A SER* 4.0 6.6 + - - -
155A THR 3.6 10.7 + - - -
156A THR* 2.9 29.7 + - - +
165A GLY* 3.7 22.6 - - - -
177A LEU 3.4 14.1 + - - -
178A ALA 3.3 1.6 + - - -
180A LEU* 1.3 77.4 - - - +
182A ALA* 1.3 58.9 + - - +
184A LYS* 3.5 9.5 + - - +
186A ALA* 2.8 27.2 + - - +
189A MET* 3.8 9.5 - - - +
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Residues in contact with ALA 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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178A ALA* 2.8 22.7 + - + +
179A MET 3.7 0.4 - - - +
181A SER* 1.3 70.9 - - - +
183A ARG* 1.3 62.3 + - + +
184A LYS 3.1 1.3 - - - -
185A GLY* 3.0 17.7 + - - -
186A ALA* 3.4 17.5 + - - +
189A MET* 5.4 2.6 - - + +
215A ASN* 3.6 34.5 - - + +
217A VAL* 4.0 13.2 - - + -
271A ARG* 4.8 9.0 + - - +
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Residues in contact with ARG 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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179A MET* 2.8 54.8 + - - +
180A LEU* 4.3 2.2 - - - +
182A ALA* 1.3 70.1 - - + +
184A LYS* 1.3 60.6 + - + +
185A GLY* 3.0 6.4 + - - -
214A ASP 5.7 0.8 + - - -
215A ASN* 5.2 3.2 - - - +
276A LEU* 6.6 0.2 - - + -
278A LYS* 3.3 42.2 - - - +
280A ARG* 4.2 25.8 - - - +
475B PRO* 5.1 2.6 - - - +
476B GLU* 2.8 33.1 + - - -
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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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154A SER* 5.1 5.6 + - - -
156A THR* 4.1 25.6 + - + +
163A LYS* 3.7 22.3 + - + -
180A LEU* 3.2 48.8 + - - +
181A SER 3.7 7.4 - - - +
182A ALA 3.1 1.4 - - - -
183A ARG* 1.3 76.8 - - - +
185A GLY* 1.3 57.0 + - - +
186A ALA 3.7 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