Contacts of the helix formed by residues 318 - 327 (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 PRO 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SER* 5.5 1.6 - - - +
206B GLU 6.0 1.3 - - - +
316B GLY 3.5 5.4 - - - +
317B ILE* 1.3 98.5 - - + +
319B LEU* 1.3 64.9 + - - +
321B VAL* 3.3 15.5 + - + -
322B ILE* 3.3 17.7 + - - +
462B HIS* 3.5 37.0 - - + +
465B LEU* 3.9 14.4 - - + -
224C ARG* 3.5 27.1 - - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 3.3 33.2 - - + -
317B ILE 3.7 0.6 + - - +
318B PRO* 1.3 68.5 - - - +
320B SER* 1.3 65.5 - - - +
322B ILE* 3.1 8.5 + - + +
323B GLU* 3.0 24.4 + - - +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PRO* 4.4 0.2 - - - +
319B LEU* 1.3 78.6 - - - +
321B VAL* 1.3 60.5 + - - +
323B GLU* 3.5 14.6 + - - +
324B ALA* 2.9 28.1 + - - +
459B PRO* 4.0 9.5 - - - +
460B SER* 4.7 2.7 + - - -
462B HIS* 2.7 35.0 + - - -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 3.7 23.6 - - - +
206B GLU 5.7 2.5 - - - +
272B VAL* 4.0 17.6 - - + +
274B LEU* 4.8 0.4 - - + -
317B ILE* 3.6 16.8 - - + -
318B PRO* 3.3 32.3 + - + +
319B LEU 3.1 0.8 - - - -
320B SER* 1.3 75.7 - - - +
322B ILE* 1.3 60.3 + - - +
324B ALA* 3.1 2.1 + - - +
325B ALA* 2.8 28.2 + - - +
459B PRO* 4.0 15.0 - - + -
460B SER 3.9 21.8 - - - +
224C ARG* 5.9 0.4 - - - +
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Residues in contact with ILE 322 (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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274B LEU* 5.1 8.1 - - + -
303B PRO 4.7 0.7 - - - +
309B ILE* 3.6 36.3 - - + +
312B ALA* 3.6 27.6 - - + -
313B ILE* 3.6 30.1 - - + -
317B ILE* 3.7 17.9 - - + +
318B PRO 3.3 13.2 + - - +
319B LEU* 3.1 11.3 + - + +
321B VAL* 1.3 77.7 - - - +
323B GLU* 1.3 61.5 + - - +
325B ALA* 3.1 10.5 + - - +
326B GLN* 3.1 32.3 + - - +
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Residues in contact with GLU 323 (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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319B LEU 3.0 16.6 + - - +
320B SER* 3.6 12.9 - - - +
322B ILE* 1.3 74.9 - - - +
324B ALA* 1.3 64.7 + - - +
326B GLN* 3.2 27.4 + - - +
327B GLN* 3.2 33.0 + - - +
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Residues in contact with ALA 324 (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* 4.1 4.7 - - + -
320B SER 2.9 19.1 + - - +
321B VAL 3.5 4.9 - - - +
323B GLU* 1.3 77.2 - - - +
325B ALA* 1.3 63.8 + - - +
327B GLN* 3.1 21.7 + - - +
328B SER* 3.2 11.4 + - - -
457B VAL* 3.7 16.3 - - + +
459B PRO* 3.7 32.8 - - + -
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Residues in contact with ALA 325 (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* 3.6 31.9 - - + +
274B LEU* 4.1 14.6 - - + +
303B PRO* 3.3 28.6 - - + +
321B VAL 2.8 13.4 + - - +
322B ILE* 3.3 11.7 - - - +
324B ALA* 1.3 78.2 - - - +
326B GLN* 1.3 60.4 + - - +
327B GLN 3.4 0.5 + - - -
328B SER* 3.4 14.0 + - - -
331B TYR* 4.7 3.3 - - - +
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Residues in contact with GLN 326 (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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303B PRO* 2.9 35.8 + - - +
304B ASN* 3.7 31.9 + - - +
309B ILE* 3.3 18.2 - - - +
322B ILE* 3.1 19.1 + - - +
323B GLU* 3.5 20.0 - - - +
324B ALA 3.1 0.8 - - - -
325B ALA* 1.3 76.5 - - - +
327B GLN* 1.3 59.0 + - + +
328B SER 3.5 0.6 + - - -
332B LYS* 4.7 7.6 + - - -
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Residues in contact with GLN 327 (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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323B GLU* 3.2 38.3 + - - +
324B ALA* 3.1 9.1 + - - +
326B GLN* 1.3 77.3 - - - +
328B SER* 1.3 62.1 + - - +
329B PRO* 3.5 8.1 - - - +
332B LYS* 4.6 10.3 - - - +
446B TYR* 4.4 11.5 + - - +
457B VAL* 3.7 25.4 - - + +
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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