Contacts of the helix formed by residues 207 - 213 (chain A) in PDB entry 3I5Y
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 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 2.7 53.7 + - - +
119A LYS* 4.0 9.8 - - - +
120A ALA* 3.9 16.4 - - + -
123A ARG* 4.1 10.9 + - - +
203A ILE 3.4 2.2 + - - -
204A HIS 3.0 11.9 + - - +
205A ASP 3.3 1.2 - - - -
206A MET* 1.3 81.6 - - - +
208A TYR* 1.3 58.7 + - - +
209A GLY* 2.8 22.5 + - - -
210A LEU* 2.9 24.5 + - + +
211A LYS 4.1 0.2 + - - -
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Residues in contact with TYR 208 (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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204A HIS 3.7 11.2 - - - -
205A ASP* 3.8 36.0 + - - -
207A ASN* 1.3 70.4 + - - +
209A GLY* 1.3 60.8 + - - +
210A LEU 3.2 0.4 - - - -
211A LYS* 3.4 41.9 + - + +
212A LYS 4.8 0.3 + - - -
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Residues in contact with GLY 209 (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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116A GLU* 4.8 8.5 - - - -
207A ASN* 2.8 14.6 + - - -
208A TYR* 1.3 79.0 - - - +
210A LEU* 1.3 61.4 + - - +
211A LYS 3.3 0.2 - - - -
212A LYS* 3.4 24.4 + - - +
213A TYR* 4.7 1.9 - - - -
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Residues in contact with LEU 210 (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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116A GLU* 3.6 21.3 - - + +
117A ILE* 3.8 10.3 - - + -
120A ALA* 3.6 31.0 - - + -
167A PHE* 4.1 13.2 - - + -
171A ILE* 3.9 19.5 - - + -
203A ILE* 3.6 17.0 - - + +
204A HIS* 3.3 18.0 + - + -
207A ASN* 2.9 20.2 + - + +
209A GLY* 1.3 73.4 - - - +
211A LYS* 1.3 64.6 + - - +
212A LYS 3.2 3.1 - - - -
213A TYR* 3.0 42.9 + - + +
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Residues in contact with LYS 211 (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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204A HIS* 3.9 35.8 + - + +
205A ASP* 4.6 9.8 + - - -
207A ASN 4.1 0.2 + - - -
208A TYR* 3.4 51.6 - - + +
209A GLY 3.3 1.0 - - - -
210A LEU* 1.3 78.4 - - - +
212A LYS* 1.3 61.8 + - - +
213A TYR 3.1 1.8 + - - -
214A ALA* 3.6 16.3 + - - +
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Residues in contact with LYS 212 (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 LYS* 3.5 29.5 - - + +
178A GLN 5.6 0.2 - - - +
208A TYR 4.8 0.4 + - - -
209A GLY 3.4 20.5 + - - +
211A LYS* 1.3 77.1 - - - +
213A TYR* 1.3 92.7 - - + +
214A ALA* 3.2 8.7 + - - +
234A LEU 5.7 0.3 - - - +
235A ARG 5.7 0.7 - - - +
237A ASN* 3.7 8.1 - - - +
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Residues in contact with TYR 213 (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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167A PHE* 3.9 18.8 - + + -
170A LEU* 3.6 40.4 - - + -
171A ILE* 3.6 32.8 - - + +
174A LYS* 3.6 38.1 + - + +
204A HIS* 3.0 19.9 + - - -
209A GLY 4.7 1.1 - - - -
210A LEU* 3.0 38.4 + - + +
211A LYS 3.7 2.2 - - - -
212A LYS* 1.3 97.2 - - + +
214A ALA* 1.3 64.2 + - - +
215A CYS* 4.9 0.3 - - - +
237A ASN* 3.6 15.5 - - - -
238A ILE* 4.8 2.8 - - - +
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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