Contacts of the helix formed by residues 211 - 215 (chain F) in PDB entry 4GG6
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 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F ILE* 3.9 26.5 - - + +
152F GLN* 3.3 39.4 + - + +
153F LYS* 4.2 2.4 - - - +
154F ALA* 4.4 10.3 - - - -
209F VAL 3.8 0.8 + - - -
210F SER* 1.3 73.4 - - - +
212F THR* 1.3 52.7 + - - +
214F TRP* 3.2 4.3 + - - +
215F GLN* 2.8 37.5 + - - +
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Residues in contact with THR 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F SER* 3.3 5.9 + - - -
211F ALA* 1.3 78.9 - - - +
213F PHE* 1.3 60.5 + - - +
215F GLN* 4.1 7.9 - - - +
216F ASN* 3.6 18.4 + - - +
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Residues in contact with PHE 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F VAL* 3.9 19.3 - - + -
175F ASN* 4.9 4.3 - - - -
209F VAL* 4.1 14.6 - - + -
210F SER* 3.1 27.2 + - - +
212F THR* 1.3 77.9 - - - +
214F TRP* 1.3 60.9 + - - +
216F ASN* 3.4 6.8 - - - +
219F ASN* 2.6 58.1 + - - +
221F PHE* 3.7 28.7 - + - -
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Residues in contact with TRP 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F GLU* 3.8 33.2 - - + -
143F PRO* 3.6 29.4 + - + +
148F ILE* 4.0 25.6 - - + +
154F ALA* 3.9 15.0 - - + -
156F LEU* 3.7 30.7 - - + -
209F VAL* 4.3 4.7 - - + -
210F SER 3.1 11.5 + - - +
211F ALA 3.7 5.8 - - - +
213F PHE* 1.3 74.3 - - - +
215F GLN* 1.3 58.9 + - + +
216F ASN 3.0 11.6 + - - +
221F PHE* 3.6 30.5 - + - -
252F ALA* 4.9 2.2 - - + -
253F TRP 3.2 27.1 - - - -
254F GLY* 3.3 24.8 - - - -
255F ARG* 3.4 23.3 + - + +
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Residues in contact with GLN 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F ALA 2.8 21.6 + - - +
212F THR* 3.7 8.9 + - - +
213F PHE 3.4 0.2 - - - -
214F TRP* 1.3 72.8 - - + +
216F ASN* 1.3 57.5 + - - +
217F PRO* 3.3 12.1 - - - +
255F ARG 3.2 17.5 - - - +
256F ALA* 3.4 22.5 - - + +
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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