Contacts of the helix formed by residues 328 - 335 (chain B) 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 SER 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLY* 3.3 11.3 - - - -
272B VAL 2.9 34.6 + - - -
324B ALA 3.2 5.8 + - - -
325B ALA 3.4 14.4 + - - -
326B GLN 3.5 0.8 - - - -
327B GLN* 1.3 75.1 - - - +
329B PRO* 1.3 66.3 - - - +
330B VAL* 3.3 5.0 + - - +
331B TYR* 3.2 20.0 + - - +
332B LYS* 3.3 24.7 + - - +
457B VAL* 4.8 0.7 - - - -
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Residues in contact with PRO 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 4.0 15.7 - - + -
270B LEU 3.6 22.7 - - - +
327B GLN 3.5 8.9 - - - +
328B SER* 1.3 84.9 - - - +
330B VAL* 1.3 58.3 + - - +
332B LYS* 3.3 6.0 + - + +
333B MET* 3.0 37.0 + - + +
446B TYR* 3.7 23.6 - - + -
454B ASP 3.6 22.9 - - - +
455B ARG 3.8 7.2 - - - +
457B VAL* 3.7 16.2 - - + -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 3.6 14.1 - - - +
9B MET 4.6 0.7 - - - +
10B VAL* 3.9 27.1 - - + +
269B TYR* 3.6 22.0 - - + +
270B LEU 3.9 1.1 - - - -
271B GLY 3.3 29.6 - - - +
273B LEU* 3.8 30.1 - - + -
328B SER* 3.1 7.8 - - - +
329B PRO* 1.3 77.2 - - - +
331B TYR* 1.3 65.4 + - - +
333B MET* 3.4 1.4 + - - +
334B ALA* 2.9 26.1 + - + +
352B MET 6.0 0.2 - - - +
354B TRP* 6.4 0.4 - - + -
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Residues in contact with TYR 331 (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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272B VAL 4.6 0.9 - - - +
273B LEU* 3.9 21.5 - - + +
274B LEU 6.1 0.4 - - - -
300B PHE* 5.2 3.1 - - + -
301B LEU 3.5 22.4 - - - -
302B ASP* 3.6 26.3 + - - +
303B PRO* 3.7 23.3 - - + -
304B ASN* 5.8 1.8 - - - -
325B ALA 4.7 3.1 - - - +
328B SER* 3.2 26.2 + - - +
330B VAL* 1.3 78.4 - - - +
332B LYS* 1.3 58.5 + - + +
334B ALA* 5.0 0.2 - - - -
335B MET* 2.7 76.4 + - + +
336B GLU* 4.2 22.7 - - + -
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Residues in contact with LYS 332 (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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326B GLN 4.7 10.9 + - - -
327B GLN* 4.6 7.9 - - - +
328B SER 3.3 18.2 + - - +
329B PRO* 3.7 5.8 - - + +
330B VAL 3.3 0.2 - - - -
331B TYR* 1.3 78.5 - - + +
333B MET* 1.3 58.7 + - - +
336B GLU* 3.2 31.5 + - - +
337B TRP* 2.8 62.6 + - + -
442B GLU* 3.1 29.2 + - - +
446B TYR* 3.3 29.8 - - + -
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Residues in contact with MET 333 (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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10B VAL* 3.8 25.6 - - + -
12B ASN* 6.2 0.2 - - - -
269B TYR* 3.3 47.3 - - + -
329B PRO* 3.0 27.4 + - + +
330B VAL 4.0 2.2 - - - +
332B LYS* 1.3 78.0 - - - +
334B ALA* 1.3 56.1 + - - +
337B TRP* 3.7 20.9 - - + -
338B LYS 3.3 2.8 + - - -
339B LEU* 2.7 41.3 + - + +
340B ALA* 3.0 18.5 + - + +
356B VAL* 4.7 4.7 - - - -
446B TYR* 4.5 10.8 - - + -
447B LEU* 4.4 16.4 - - + -
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Residues in contact with ALA 334 (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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10B VAL* 5.3 0.4 - - + -
273B LEU* 5.7 1.6 - - + -
293B TYR* 4.7 0.5 + - - -
297B LEU* 3.6 14.6 - - + +
300B PHE* 4.9 7.0 - - + -
330B VAL* 2.9 22.2 + - + +
331B TYR* 4.4 0.9 - - - +
333B MET* 1.3 80.0 - - - +
335B MET* 1.3 63.2 + - + +
338B LYS* 3.5 21.2 - - - +
340B ALA* 4.1 14.2 - - + +
354B TRP* 3.8 29.6 - - + -
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Residues in contact with MET 335 (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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273B LEU* 5.4 0.2 - - + -
297B LEU* 3.5 41.7 - - + +
300B PHE* 4.0 21.1 - - + +
331B TYR* 2.7 61.2 + - + +
334B ALA* 1.3 75.7 - - + +
336B GLU* 1.3 59.9 + - - +
338B LYS* 3.1 32.7 - - - -
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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