Contacts of the helix formed by residues 199 - 203 (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 TYR 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B SER* 4.7 1.1 - - - -
172B PRO 3.2 3.4 + - - -
173B CYS* 3.1 2.1 - - - -
174B ALA* 2.9 19.1 + - - -
197B LYS* 3.4 32.5 - - + +
198B ALA* 1.3 77.7 - - - +
200B ALA* 1.3 66.2 + - - +
202B SER* 3.0 13.8 + - - -
203B MET 3.5 33.0 - - - +
204B PHE* 3.5 22.2 - - + -
205B ASP* 3.4 31.1 + - + +
208B ASP* 4.6 1.7 + - - +
209B ASP* 5.4 2.2 + - - -
421B HIS* 2.8 43.8 + - - -
428B ASN* 3.5 15.9 - - - -
431B ASP* 3.4 17.3 - - - +
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Residues in contact with ALA 200 (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 CYS* 4.2 3.8 - - - -
174B ALA* 3.8 10.4 - - - +
199B TYR* 1.3 69.5 - - - +
201B GLY* 1.3 61.6 + - - +
202B SER 3.3 1.0 + - - -
203B MET* 3.4 18.0 + - - +
255B ALA* 4.0 9.5 - - + +
418B TYR* 4.0 14.8 - - - +
430B ILE* 4.4 10.0 - - + +
431B ASP* 2.8 22.3 + - - +
434B VAL* 4.2 24.5 - - + -
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B CYS* 3.5 10.8 - - - -
199B TYR 3.2 1.2 + - - -
200B ALA* 1.3 67.6 - - - +
202B SER* 1.3 73.1 + - - +
203B MET* 3.1 9.7 + - - +
253B CYS* 4.0 7.0 - - - -
255B ALA* 3.5 16.0 - - - +
256B HIS* 2.9 37.5 + - - -
263B ALA 5.0 1.2 - - - +
266B ALA* 4.7 2.1 - - - +
267B ALA 4.9 1.6 + - - -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B SER 4.2 10.9 - - - +
172B PRO 4.1 8.3 - - - -
173B CYS* 3.5 9.4 + - - +
199B TYR* 3.0 15.8 + - - -
201B GLY* 1.3 81.7 - - - +
203B MET* 1.3 59.2 + - - +
204B PHE* 2.8 24.7 + - - +
239B ALA* 5.0 1.5 - - - +
240B VAL 2.6 29.8 + - - -
241B TYR* 4.1 5.4 - - - +
263B ALA 5.7 0.2 + - - -
267B ALA* 4.2 18.8 - - - +
270B GLN* 4.3 4.7 - - - +
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Residues in contact with MET 203 (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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199B TYR* 3.5 18.5 - - - +
200B ALA 3.4 17.3 + - - +
201B GLY* 3.9 10.1 - - - +
202B SER* 1.3 73.1 - - - +
204B PHE* 1.3 66.0 + - - +
256B HIS* 4.3 8.3 - - + -
266B ALA* 4.0 35.4 - - + +
270B GLN* 3.5 30.6 + - - +
273B LYS* 6.0 2.5 - - - +
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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