Contacts of the helix formed by residues 203 - 213 (chain A) in PDB entry 4IYM
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 2.9 42.7 + - - -
35A LEU* 4.0 10.6 - - + +
36A ALA 5.5 0.5 + - - +
171A LYS* 4.7 1.6 - - - +
174A GLU* 3.4 20.4 - - + +
202A GLY* 1.3 75.3 - - - -
204A LYS* 1.3 67.8 + - + +
205A GLY* 3.0 15.1 + - - -
206A ALA* 3.1 12.4 + - - +
207A VAL* 3.2 17.6 + - - +
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Residues in contact with LYS 204 (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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203A ASP* 1.3 79.3 - - - +
205A GLY* 1.3 56.6 + - - +
207A VAL* 3.3 9.7 + - + +
208A ASP* 2.8 58.4 + - - +
230A TYR* 3.1 34.6 + - + -
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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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17A ARG* 5.3 3.6 - - - -
36A ALA 4.8 4.7 - - - -
38A ASP* 4.2 8.0 - - - +
203A ASP* 3.0 12.1 + - - -
204A LYS* 1.3 78.0 - - - +
206A ALA* 1.3 56.2 + - - +
208A ASP* 3.4 6.6 + - - +
209A ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 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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36A ALA* 4.2 26.6 + - + +
37A SER 5.7 0.9 - - - -
41A LEU* 4.6 3.9 - - + +
171A LYS* 4.1 13.5 - - + -
200A VAL* 4.8 5.4 - - + -
201A ASN 4.4 0.7 - - - +
202A GLY* 3.9 21.5 - - - -
203A ASP* 3.1 11.1 + - - +
205A GLY* 1.3 74.2 - - - +
207A VAL* 1.3 57.8 + - - +
209A ALA* 3.3 8.5 + - - +
210A ILE* 3.0 35.1 + - + +
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Residues in contact with VAL 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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144A ILE* 3.8 35.7 - - + -
171A LYS* 3.7 24.0 - - + -
203A ASP 3.2 14.6 + - - +
204A LYS* 3.6 11.7 - - + +
206A ALA* 1.3 77.1 - - - +
208A ASP* 1.3 65.1 + - - +
210A ILE* 3.2 11.1 + - - +
211A LEU* 3.0 37.6 + - + +
227A ILE* 6.1 1.3 - - + -
230A TYR* 5.2 4.0 - - + -
231A VAL* 4.2 11.0 - - + -
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Residues in contact with ASP 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 LYS* 2.8 48.1 + - - +
205A GLY* 3.8 5.8 - - - +
207A VAL* 1.3 73.0 - - - +
209A ALA* 1.3 62.2 + - - +
211A LEU* 3.3 8.7 + - - +
212A THR* 3.1 35.1 + - + +
230A TYR* 2.7 30.2 + - - -
234A THR* 5.3 1.0 - - - +
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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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38A ASP* 3.7 27.8 - - + +
41A LEU* 3.9 24.0 - - + +
205A GLY 3.0 14.5 + - - +
206A ALA* 3.5 10.8 - - - +
207A VAL 3.3 0.4 - - - -
208A ASP* 1.3 75.2 - - - +
210A ILE* 1.3 62.1 + - - +
212A THR* 3.5 7.0 + - - -
213A HIS* 3.2 25.1 + - - +
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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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41A LEU* 3.7 25.6 - - + -
142A ALA* 3.6 32.1 - - + -
143A GLY 5.3 0.2 - - - +
144A ILE* 4.8 8.1 - - + -
169A ILE* 4.7 5.8 - - + -
171A LYS* 3.8 33.7 - - + +
200A VAL* 5.8 0.7 - - + -
206A ALA* 3.0 19.7 + - + +
207A VAL* 3.2 10.3 + - - +
209A ALA* 1.3 76.2 - - - +
211A LEU* 1.3 64.7 + - + +
213A HIS 3.3 10.0 + - - -
216A ILE* 3.7 18.9 - - + +
219A VAL* 4.3 17.3 - - + -
240A LYS* 3.3 11.3 - - - -
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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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144A ILE* 5.0 1.8 - - + -
207A VAL* 3.0 37.5 + - + +
208A ASP* 3.3 15.5 + - - +
210A ILE* 1.3 79.5 - - + +
212A THR* 1.3 60.4 + - + +
219A VAL* 4.2 15.0 - - + -
230A TYR* 4.3 7.2 - - + -
231A VAL* 3.8 34.1 - - + +
234A THR* 3.9 32.5 - - + +
235A ALA* 3.9 18.1 - - + +
238A ASN* 3.2 16.2 - - - +
240A LYS* 2.8 22.6 + - - +
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Residues in contact with THR 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 ASP* 3.1 22.7 + - + +
209A ALA* 3.5 9.5 + - - -
211A LEU* 1.3 82.5 - - + +
213A HIS* 1.3 62.3 + - - +
214A PRO* 3.4 8.7 - - - +
234A THR* 5.5 3.8 - - + -
238A ASN* 3.6 23.3 - - - +
240A LYS* 4.0 1.3 - - - -
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Residues in contact with HIS 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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41A LEU* 3.8 21.5 - - + -
42A ALA* 4.2 17.5 + - + +
45A VAL* 3.4 33.8 - - + +
46A GLU* 4.8 5.0 + - - -
209A ALA 3.2 15.8 + - - +
210A ILE 3.3 8.7 + - - +
212A THR* 1.3 75.2 - - - +
214A PRO* 1.4 72.3 - - + +
215A ASP* 3.2 36.1 + - - +
216A ILE* 3.3 16.7 + - + -
240A LYS* 2.7 24.5 + - - -
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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