Contacts of the helix formed by residues 208 - 222 (chain A) in PDB entry 1ISS
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A THR* 2.6 45.2 + - - +
189A SER* 3.8 6.9 + - - -
190A ILE* 3.8 17.4 + - + +
207A SER* 1.3 75.1 + - - +
209A THR* 1.3 69.2 + - - +
210A LEU 3.1 0.7 - - - -
211A GLN* 2.7 41.8 + - + +
212A ALA* 3.4 3.5 + - - +
236A TYR* 3.8 23.6 - - - +
240A GLY* 5.3 0.4 - - - +
290A PHE* 4.1 18.0 - - + -
318A ASP* 4.9 0.9 - - - +
479A TYR* 5.1 0.5 + - - -
1001A MCG 4.8 1.2 - - - +
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Residues in contact with THR 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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190A ILE* 3.5 32.1 - - + +
193A SER* 5.5 1.7 + - - -
207A SER* 2.5 22.2 + - - -
208A ASP* 1.3 71.5 - - - +
210A LEU* 1.3 65.2 + - + +
211A GLN 2.8 6.9 + - - -
212A ALA* 3.1 13.0 + - - +
213A ARG* 3.2 11.0 + - + +
243A ALA* 5.0 10.1 - - + -
247A LEU* 5.2 4.6 - - + +
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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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206A PRO* 3.6 16.6 - - + -
207A SER* 3.6 12.0 + - - +
208A ASP 3.1 0.6 - - - -
209A THR* 1.3 81.8 - - + +
211A GLN* 1.3 60.1 + - - +
213A ARG* 3.9 13.5 - - + +
214A ALA* 3.3 21.5 + - - +
475A ALA 4.4 4.7 - - - +
476A PRO* 5.0 0.7 - - + -
477A GLY* 3.5 30.7 - - - +
479A TYR* 4.2 13.5 - - + +
500A TRP* 4.2 24.7 - - + -
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Residues in contact with GLN 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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208A ASP* 2.7 39.6 + - - +
210A LEU* 1.3 70.4 - - - +
212A ALA* 1.3 66.1 + - - +
214A ALA* 3.0 6.0 + - - +
215A MET* 2.8 28.3 + - - +
236A TYR* 3.9 2.6 + - - -
290A PHE* 4.1 13.4 - - + -
317A SER* 3.4 18.2 - - - -
318A ASP* 2.6 53.8 + - - +
340A ILE* 3.6 16.5 - - + +
479A TYR* 3.8 27.1 - - + +
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Residues in contact with ALA 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 3.4 2.3 + - - +
209A THR 3.1 7.5 + - - +
211A GLN* 1.3 75.2 - - - +
213A ARG* 1.3 68.5 + - - +
215A MET* 2.7 12.3 + - - -
216A LEU* 2.7 25.1 + - - +
240A GLY 4.1 7.6 - - - +
243A ALA* 4.2 5.2 - - + -
244A PHE* 3.7 43.9 - - + +
247A LEU* 3.8 8.1 - - + -
290A PHE* 4.3 4.3 - - + -
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Residues in contact with ARG 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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209A THR* 3.2 14.6 + - + +
210A LEU* 3.9 16.8 - - + +
212A ALA* 1.3 79.6 - - - +
214A ALA* 1.3 55.6 + - - +
216A LEU* 3.3 8.1 + - - +
217A ASP* 2.6 69.3 + - - +
220A LYS* 3.9 20.2 - - - +
247A LEU* 3.7 28.5 - - + +
251A GLU* 3.5 25.3 + - - -
500A TRP* 3.7 21.3 - - + -
503A GLY* 5.6 4.2 + - - -
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Residues in contact with ALA 214 (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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210A LEU 3.3 13.5 + - - +
211A GLN* 3.0 5.8 + - - +
213A ARG* 1.3 77.4 - - - +
215A MET* 1.3 63.7 + - - +
217A ASP* 3.7 2.5 + - - +
218A ILE* 3.2 28.1 + - - +
340A ILE* 4.6 15.3 - - + -
479A TYR* 5.4 2.0 - - + -
481A ILE* 5.6 1.1 - - + -
500A TRP* 3.1 46.7 + - + +
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Residues in contact with MET 215 (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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211A GLN* 2.8 20.5 + - - +
212A ALA* 2.7 15.6 + - - +
214A ALA* 1.3 69.8 - - - +
216A LEU* 1.3 64.1 + - - +
218A ILE* 2.9 22.0 + - - +
219A VAL* 3.0 11.8 + - + +
244A PHE* 4.3 9.4 - - + -
288A VAL* 4.4 12.8 - - + -
289A CYS 3.9 9.6 - - - +
290A PHE* 4.1 23.1 - - - +
315A ILE* 3.5 30.7 - - + +
316A GLY 3.5 2.7 - - - +
317A SER* 3.4 37.0 - - - +
340A ILE* 3.4 26.5 - - + -
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Residues in contact with LEU 216 (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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212A ALA 2.7 16.3 + - - +
213A ARG* 3.6 12.6 - - - +
215A MET* 1.3 68.2 - - - +
217A ASP* 1.3 55.9 + - - +
218A ILE 2.6 16.0 + - - -
219A VAL* 2.7 20.3 + - + +
220A LYS* 2.7 22.8 + - + +
244A PHE* 3.1 34.2 - - + -
247A LEU* 3.3 48.2 - - + +
248A ALA* 5.4 1.1 - - - -
251A GLU* 3.8 15.3 - - + -
253A LEU* 4.0 22.9 - - + -
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Residues in contact with ASP 217 (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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213A ARG* 2.6 76.8 + - - +
214A ALA 3.7 6.7 - - - +
215A MET 3.3 0.2 - - - -
216A LEU* 1.3 70.4 - - - +
218A ILE* 1.3 62.1 + - - +
220A LYS* 3.3 22.7 + - + +
221A ARG* 3.3 13.0 + - - +
500A TRP* 4.1 12.3 + - - +
503A GLY* 3.8 19.6 - - - +
505A LEU* 3.0 25.7 - - + +
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Residues in contact with ILE 218 (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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214A ALA 3.2 15.3 + - - +
215A MET* 2.9 9.1 + - - +
216A LEU 2.6 5.1 + - - -
217A ASP* 1.3 69.6 - - - +
219A VAL* 1.3 70.0 + - - +
220A LYS 2.7 3.0 + - - -
221A ARG* 2.8 13.5 + - - +
222A TYR* 3.4 30.4 + - + -
224A TRP* 5.1 1.8 - - + -
315A ILE* 4.7 18.6 - - + -
338A ILE* 4.5 19.3 - - + -
340A ILE* 3.6 13.2 - - + -
481A ILE* 3.6 40.4 - - + -
505A LEU* 3.6 20.4 - - + -
507A ILE* 5.2 4.9 - - + -
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Residues in contact with VAL 219 (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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215A MET* 3.6 11.9 - - + +
216A LEU* 2.7 18.7 + - + +
218A ILE* 1.3 74.1 - - - +
220A LYS* 1.3 62.4 + - - +
222A TYR* 3.4 8.1 + - - +
223A ASN* 3.6 6.2 + - - -
224A TRP* 3.7 41.5 + - + +
227A VAL* 3.9 20.6 - - + -
244A PHE* 4.6 3.8 - - + -
253A LEU* 4.3 11.2 - - + -
288A VAL* 4.5 15.9 - - + -
315A ILE* 3.9 25.1 - - + -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ARG* 3.9 25.0 - - - +
216A LEU* 2.7 24.5 + - + +
217A ASP* 3.3 33.6 + - - +
218A ILE 2.7 0.8 + - - -
219A VAL* 1.3 72.9 - - - +
221A ARG* 1.3 64.3 + - - +
223A ASN* 2.8 22.5 + - - +
251A GLU* 4.4 18.3 + - + +
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Residues in contact with ARG 221 (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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217A ASP 3.3 8.1 + - - +
218A ILE 2.8 12.8 + - - +
220A LYS* 1.3 75.9 - - - +
222A TYR* 1.3 68.3 + - + +
223A ASN* 3.4 13.5 + - - -
505A LEU* 3.7 31.5 + - + +
506A ASN* 5.2 0.6 - - - +
507A ILE* 3.7 45.2 + - - +
509A ASP* 3.6 32.8 + - - -
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Residues in contact with TYR 222 (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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218A ILE* 3.4 26.1 + - + -
219A VAL 3.4 0.6 + - - +
220A LYS 3.0 1.2 - - - -
221A ARG* 1.3 98.5 - - + +
223A ASN* 1.3 57.9 + - - +
224A TRP* 2.5 70.5 + + + +
338A ILE* 5.1 7.1 - - + +
507A ILE* 3.6 17.5 - - + +
509A ASP* 4.5 8.3 + - - -
512A ILE* 3.1 40.1 - - + +
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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