Contacts of the helix formed by residues 285 - 290 (chain A) in PDB entry 1SIW
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 ALA 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ASN* 3.7 22.7 - - + +
281A THR* 4.3 4.7 + - + +
283A ASP* 3.1 28.1 + - - +
284A TYR* 1.3 74.7 - - - +
286A GLU* 1.3 68.4 + - - +
287A ILE* 3.1 11.2 - - + +
288A ALA* 3.0 20.4 + - - +
289A LYS 3.7 2.4 + - - -
1153A ARG* 4.2 6.3 - - - +
177B MET* 3.7 7.3 - - - +
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Residues in contact with GLU 286 (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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255A ASN* 3.6 7.6 - - - +
257A PRO* 3.7 13.0 - - + +
258A GLN* 3.3 42.6 + - - +
285A ALA* 1.3 74.3 - - - +
287A ILE* 1.3 63.4 + - - +
289A LYS* 3.1 22.3 + - - +
290A LEU* 3.9 4.5 + - - +
1094A LYS* 2.9 27.7 + - - -
1153A ARG* 5.4 0.9 - - - +
17B ILE 4.0 11.1 - - - +
147B ASP* 2.7 27.2 - - - +
177B MET* 3.8 8.6 - - + +
179B TYR* 3.1 24.4 + - + +
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Residues in contact with ILE 287 (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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251A ALA* 3.5 21.8 - - + -
254A SER 3.4 25.6 - - - +
255A ASN* 2.9 20.3 + - - +
256A VAL* 4.2 5.6 - - + +
257A PRO* 3.7 19.0 - - + +
267A PHE* 4.4 7.2 - - + -
279A ALA* 3.6 6.3 - - + -
281A THR* 3.8 25.8 - - + +
285A ALA* 3.1 6.7 + - + -
286A GLU* 1.3 75.9 - - - +
288A ALA* 1.3 66.8 + - - +
290A LEU* 3.1 15.4 + - + +
291A CYS* 3.2 29.3 + - - -
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Residues in contact with ALA 288 (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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279A ALA* 4.1 12.1 - - + -
281A THR* 4.9 0.7 - - - +
284A TYR* 3.9 28.5 - - + -
285A ALA 3.0 17.6 + - - +
287A ILE* 1.3 81.2 - - + +
289A LYS* 1.3 58.9 - - - +
290A LEU 3.0 1.4 + - - -
291A CYS* 3.0 5.5 + - - -
294A TRP* 4.2 23.1 - - + -
361B PRO* 2.8 30.2 - - - +
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Residues in contact with LYS 289 (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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271A ARG* 5.8 0.3 + - - -
284A TYR* 4.2 15.3 + - + +
285A ALA 3.7 2.3 + - - +
286A GLU* 3.1 19.0 + - - +
288A ALA* 1.3 78.6 - - - +
290A LEU* 1.3 68.6 + - + +
291A CYS 3.8 0.7 + - - -
13B LEU 2.8 29.0 + - - -
14B ASP* 3.5 15.2 + - - +
16B CYS* 3.0 21.5 + - - +
177B MET* 3.5 25.8 - - + +
178B MET* 4.4 11.7 - - - +
179B TYR* 4.3 22.7 - - + +
358B PRO* 4.2 11.2 - - - +
359B LEU 4.0 17.6 + - - +
360B SER* 4.2 2.0 - - - -
361B PRO* 4.0 8.5 - - - +
385B ILE* 6.2 1.8 - - + -
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Residues in contact with LEU 290 (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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257A PRO* 4.2 24.7 - - + -
264A ALA* 5.5 1.8 - - + -
267A PHE* 3.8 17.8 - - + -
268A THR* 3.7 30.1 - - + -
271A ARG* 3.1 34.3 + - - +
277A THR* 3.6 1.9 + - - -
286A GLU 4.3 4.5 - - - +
287A ILE* 3.1 7.0 + - + +
288A ALA 3.0 1.4 - - - -
289A LYS* 1.3 100.3 - - + +
291A CYS* 1.3 59.6 + - - +
14B ASP 3.7 21.5 - - - +
15B LYS 4.7 0.2 - - - +
16B CYS 4.1 7.9 - - - +
17B ILE* 4.0 17.3 - - + -
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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