Contacts of the helix formed by residues 175 - 179 (chain B) in PDB entry 2FGY
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 ASP 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B CYS* 3.1 22.1 - - + +
174B ALA* 1.3 77.1 - - - +
176B GLY* 1.3 67.3 + - - +
177B ARG* 2.8 67.9 + - - +
178B LEU* 2.9 20.3 + - + +
179B LYS* 3.9 2.4 + - - -
242B HIS* 3.4 20.1 - - + +
252B GLY 4.4 0.9 - - - +
254B ALA 5.6 0.9 + - - -
397B HIS* 3.0 22.5 + - + -
418B TYR* 4.1 9.0 - - - -
720B ZN 4.0 2.4 - - - -
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Residues in contact with GLY 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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174B ALA 3.3 3.2 + - - -
175B ASP* 1.3 71.5 + - - +
177B ARG* 1.3 57.9 + - - +
179B LYS* 3.1 18.1 + - - +
399B GLU* 2.9 30.4 + - - -
415B ASN* 2.7 25.1 + - - -
417B ALA 3.1 23.1 - - - -
418B TYR* 4.2 0.6 - - - +
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Residues in contact with ARG 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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175B ASP* 2.8 44.3 + - - +
176B GLY* 1.3 76.6 - - - +
178B LEU* 1.3 65.5 + - - +
179B LYS 3.4 0.2 - - - -
180B GLY 4.9 0.5 + - - -
185B ILE* 4.5 8.7 - - - +
242B HIS* 4.0 3.6 - - - -
251B SER* 2.9 25.8 + - - +
252B GLY 3.3 20.4 + - - -
295B VAL* 5.7 0.2 - - - +
297B THR* 3.5 29.6 + - + +
300B ASP* 4.5 1.4 - - - +
395B ILE 3.0 23.4 + - - -
396B GLY* 3.5 33.6 - - - -
397B HIS* 3.8 13.5 + - - +
414B ARG* 3.4 47.8 + - + +
415B ASN* 4.0 7.0 + - - +
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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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172B PRO* 3.8 16.5 - - + +
173B CYS* 3.6 34.3 - - + +
175B ASP* 2.9 11.9 + - + +
177B ARG* 1.3 83.5 - - - +
179B LYS* 1.3 58.0 + - - +
180B GLY 3.1 3.4 - - - -
181B LEU* 2.9 33.1 + - + +
185B ILE* 4.2 7.0 - - + -
240B VAL* 4.3 13.9 - - + +
242B HIS* 3.7 33.4 - - + -
295B VAL* 4.0 36.6 - - + -
297B THR* 4.9 2.2 - - + -
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Residues in contact with LYS 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 ASP 3.9 2.1 + - - +
176B GLY* 3.1 17.8 + - - +
177B ARG 3.4 0.2 - - - -
178B LEU* 1.3 77.6 - - - +
180B GLY* 1.3 55.2 + - - +
181B LEU* 3.3 2.3 + - - +
196B ARG* 5.4 6.1 - - - +
403B SER* 5.8 1.0 + - - -
407B GLY* 5.1 0.6 - - - -
408B PHE 4.8 11.6 + - - +
411B VAL 4.2 8.1 - - - +
412B GLN* 3.3 37.9 + - - +
413B ILE 3.2 24.0 - - - +
415B ASN 4.6 0.2 - - - +
416B LEU* 4.9 0.2 - - + -
417B ALA* 3.7 37.0 - - + +
419B TYR* 3.4 45.6 - - + +
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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