Contacts of the helix formed by residues 204 - 213 (chain A) in PDB entry 1HNY
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 PRO 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ARG* 3.5 19.3 - - - +
202A MET 3.6 1.3 - - - +
203A TRP* 1.3 88.2 - - + +
205A GLY* 1.4 58.1 + - - +
207A ILE* 3.1 3.0 + - + -
208A LYS* 2.9 25.4 + - - +
246A ASP* 3.5 35.0 - - + +
247A TYR* 4.0 21.3 - - + -
250A ASN* 3.2 22.2 + - - +
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Residues in contact with GLY 205 (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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176A ARG* 4.5 2.0 + - - -
203A TRP* 3.1 3.7 - - - +
204A PRO* 1.4 80.7 - - - +
206A ASP* 1.3 58.2 + - - +
208A LYS* 3.3 11.2 + - - +
209A ALA* 2.9 28.2 + - - +
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Residues in contact with ASP 206 (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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170A LEU* 3.4 44.5 + - + +
171A GLU* 3.5 14.5 + - - +
176A ARG* 2.9 22.2 + - - +
203A TRP* 3.0 39.6 + - + +
205A GLY* 1.3 72.3 - - - +
207A ILE* 1.3 66.1 + - + +
209A ALA* 3.1 15.4 + - - +
210A ILE* 3.1 20.7 + - - +
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Residues in contact with ILE 207 (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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99A ILE* 5.4 1.8 - - + -
170A LEU* 5.6 0.2 - - + -
196A LEU* 3.5 27.4 - - + -
199A SER* 4.0 7.9 - - - +
202A MET* 3.9 39.7 - - + -
203A TRP 3.3 10.5 + - - +
204A PRO 3.1 5.9 + - - +
206A ASP* 1.3 74.8 - - - +
208A LYS* 1.3 65.9 + - - +
210A ILE* 3.1 11.2 + - - +
211A LEU* 3.0 33.7 + - + +
232A GLN* 3.9 7.0 - - - +
247A TYR* 3.6 36.3 - - + -
250A ASN* 3.5 18.2 - - - +
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Residues in contact with LYS 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 PRO 2.9 11.5 + - - +
205A GLY* 3.4 14.1 - - - +
206A ASP 3.2 0.2 - - - -
207A ILE* 1.3 75.4 - - - +
209A ALA* 1.3 65.7 + - - +
211A LEU* 3.1 8.8 + - + +
212A ASP* 2.8 63.4 + - - +
250A ASN* 3.5 20.5 + - - +
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Residues in contact with ALA 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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176A ARG* 3.3 44.2 - - - +
205A GLY 2.9 12.2 + - - +
206A ASP 3.1 8.9 + - - +
208A LYS* 1.3 80.5 - - + +
210A ILE* 1.3 59.2 + - - +
212A ASP* 3.6 15.3 + - - +
213A LYS* 3.6 20.6 - - - +
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Residues in contact with ILE 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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99A ILE* 4.2 17.5 - - + -
170A LEU* 4.5 17.3 - - + -
176A ARG* 4.0 26.2 - - + +
179A ILE* 3.8 44.4 - - + -
180A ALA* 4.5 8.5 - - - +
183A MET* 3.8 17.7 - - - -
206A ASP 3.1 14.3 + - - +
207A ILE* 3.1 9.3 + - + +
209A ALA* 1.3 72.4 - - - +
211A LEU* 1.3 69.3 + - + +
213A LYS* 3.1 25.4 + - - +
214A LEU* 3.5 8.2 - - + +
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Residues in contact with LEU 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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1A PCA 5.8 1.1 - - + -
183A MET* 5.0 4.5 - - + -
196A LEU* 4.7 10.1 - - + -
207A ILE* 3.0 23.5 + - + +
208A LYS* 3.5 8.3 - - + +
210A ILE* 1.3 76.2 - - + +
212A ASP* 1.3 66.0 + - - +
214A LEU* 3.1 36.7 + - + +
227A LYS* 4.8 3.8 + - - -
228A PRO* 5.9 0.4 - - + -
230A ILE* 3.7 32.8 - - + -
250A ASN* 3.7 45.5 - - + +
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Residues in contact with ASP 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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208A LYS* 2.8 60.6 + - - +
209A ALA* 3.7 10.7 - - - +
210A ILE 3.2 0.2 - - - -
211A LEU* 1.3 76.2 - - - +
213A LYS* 1.3 62.0 + - + +
214A LEU 3.3 4.3 + - - +
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Residues in contact with LYS 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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173A ASP* 2.7 32.2 + - - -
176A ARG* 3.9 25.1 - - + +
177A SER* 3.5 19.5 + - - +
180A ALA* 3.4 23.1 - - + -
184A ASN* 3.1 17.7 + - - -
209A ALA 3.6 15.7 - - - +
210A ILE* 3.1 9.6 + - - +
211A LEU 3.0 1.0 - - - -
212A ASP* 1.3 80.2 - - + +
214A LEU* 1.3 60.7 + - - +
215A HIS* 4.7 2.1 - - - -
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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