Contacts of the strand formed by residues 206 - 213 (chain B) in PDB entry 1IAS
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 VAL 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B THR 4.2 7.9 - - - +
205B ILE* 1.3 81.5 - - - +
207B LEU* 1.3 60.0 - - - +
208B GLN* 2.7 37.0 + - - +
223B LYS* 2.8 30.3 + - + +
225B ARG 6.2 0.7 - - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 4.0 15.2 + - + +
206B VAL* 1.3 80.6 - - - +
208B GLN* 1.3 67.0 + - - +
220B TRP* 4.0 34.1 - - + -
222B GLY* 4.1 4.5 - - - -
231B VAL* 4.1 20.4 - - + -
233B ILE* 3.7 25.1 - - + -
277B TRP* 4.0 27.8 - - + -
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SO4 3.8 7.6 + - - -
206B VAL* 2.7 34.8 + - - +
207B LEU* 1.3 80.2 + - - +
209B GLU* 1.3 67.0 + - + +
220B TRP* 4.5 5.2 - - - -
221B ARG* 2.8 53.2 + - - +
222B GLY* 3.8 10.8 - - - -
223B LYS* 3.6 37.3 + - + +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B GLN* 1.3 84.6 - - + +
210B SER* 1.3 73.0 + - - +
211B ILE* 4.4 2.6 - - - +
220B TRP* 3.4 15.8 - - - -
221B ARG* 2.3 73.0 + - - +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLU* 1.3 89.0 - - - +
211B ILE* 1.3 60.5 + - - +
212B GLY* 3.7 10.0 + - - -
213B LYS* 5.1 1.2 - - - +
218B GLU* 2.9 29.5 + - - -
219B VAL 3.8 6.6 + - - -
220B TRP* 3.5 19.4 - - - -
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLU* 4.1 2.9 - - - +
210B SER* 1.3 76.7 - - - +
212B GLY* 1.3 59.6 + - - +
219B VAL* 2.8 25.1 + - + +
220B TRP 3.8 3.8 - - - +
221B ARG* 3.3 42.6 - - + +
230B ALA* 5.4 1.6 - - + -
282B TYR* 3.5 24.2 - - + +
286B GLY* 6.0 6.3 - - - -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 3.7 3.9 + - - -
211B ILE* 1.3 81.8 - - - +
213B LYS* 1.3 68.6 + - - +
218B GLU* 3.3 5.9 - - - +
219B VAL* 2.8 33.5 + - - +
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 5.1 2.0 - - - +
212B GLY* 1.3 79.1 - - - +
214B GLY* 1.3 60.0 + - - +
216B PHE* 3.2 18.1 - - - -
217B GLY 3.4 9.6 - - - +
218B GLU* 3.4 33.4 + - + +
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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