Contacts of the helix formed by residues 323 - 334 (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 SER 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A PHE* 2.8 23.8 + - - -
321A ASN 3.2 3.7 + - - -
322A PRO* 1.3 69.0 - - - +
324A GLN* 1.3 65.1 + - - +
325A TYR 3.6 0.7 + - - -
326A PHE* 3.4 35.2 + - - -
327A THR* 2.9 28.3 + - - -
530A ASP* 2.7 31.0 + - - -
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Residues in contact with GLN 324 (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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322A PRO 3.5 5.1 + - - -
323A SER* 1.3 70.9 + - - +
325A TYR* 1.3 65.0 + - - +
327A THR* 4.0 4.0 - - - -
328A ASP* 3.2 23.8 + - + +
530A ASP* 5.1 0.4 + - - -
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Residues in contact with TYR 325 (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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323A SER* 3.2 6.6 + - - +
324A GLN* 1.3 82.4 - - - +
326A PHE* 1.3 85.8 + + + +
328A ASP* 3.8 5.4 - - - +
329A TYR* 2.9 40.0 + + + +
529A ALA 4.4 0.9 - - - -
530A ASP* 4.3 7.8 + - - +
533A HIS* 3.3 64.1 + + + +
534A GLY 3.8 0.2 - - - -
564A CYS 3.7 8.3 - - - -
565A GLY* 2.7 33.6 + - - -
569A GLN* 2.8 27.2 + - - +
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Residues in contact with PHE 326 (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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317A PHE* 3.7 35.9 - + + +
318A HIS* 3.7 13.7 - + + +
323A SER* 3.3 23.2 + - - +
325A TYR* 1.3 92.5 - + - +
327A THR* 1.3 57.9 + - - +
329A TYR* 3.1 7.7 + - - +
330A VAL* 2.9 33.8 + - - +
526A ALA* 3.3 22.9 - - + -
529A ALA* 3.8 5.8 - - + -
530A ASP* 3.5 22.2 - - + -
563A PHE 3.4 19.7 - - - +
564A CYS* 3.2 37.5 - - + -
565A GLY 5.2 0.9 - - - +
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Residues in contact with THR 327 (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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317A PHE 5.0 0.2 + - - -
318A HIS* 4.4 10.8 + - - -
322A PRO* 4.3 12.0 - - + +
323A SER 2.9 31.6 + - - -
324A GLN* 4.0 4.5 - - - -
326A PHE* 1.3 73.1 - - - +
328A ASP* 1.3 63.2 + - - +
330A VAL* 3.2 10.4 - - - +
331A ARG* 3.1 46.4 + - - +
417A LEU* 4.1 12.2 - - + +
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Residues in contact with ASP 328 (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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324A GLN* 3.2 17.9 + - + +
325A TYR* 3.8 5.4 - - + +
327A THR* 1.3 80.3 - - - +
329A TYR* 1.3 65.2 + - - +
331A ARG* 3.2 14.3 + - - +
332A ARG* 3.0 65.2 + - - +
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Residues in contact with TYR 329 (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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325A TYR* 2.9 35.1 + + + +
326A PHE* 3.4 5.8 - - - +
328A ASP* 1.3 81.3 + - - +
330A VAL* 1.3 61.8 + - + +
333A TYR* 2.9 56.6 + + + +
334A THR* 4.8 0.2 - - + -
562A ILE* 3.6 21.5 - - + -
565A GLY* 3.4 38.6 - - - -
567A VAL* 2.6 39.5 + - - +
569A GLN* 5.1 0.7 - - + -
1029A VAL* 4.4 8.7 - - + +
1042A GLN* 2.9 32.1 + - - -
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Residues in contact with VAL 330 (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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318A HIS* 4.0 21.8 - - + +
326A PHE 2.9 20.1 + - - +
327A THR* 3.2 21.3 - - - +
329A TYR* 1.3 72.6 - - + +
331A ARG* 1.3 63.1 + - - +
334A THR* 2.5 40.3 + - + +
336A MET* 3.9 27.6 - - - -
337A PRO* 4.2 4.0 - - - +
417A LEU* 4.1 16.9 - - + +
474A TYR* 5.1 1.3 - - + -
562A ILE* 3.9 22.0 - - + +
563A PHE* 4.4 6.1 - - + +
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Residues in contact with ARG 331 (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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327A THR* 3.1 41.1 + - - +
328A ASP* 3.4 13.6 + - - +
329A TYR 3.1 0.2 - - - -
330A VAL* 1.3 79.7 - - - +
332A ARG* 1.3 66.9 + - - +
337A PRO* 4.0 8.2 - - - +
379A THR* 5.9 0.8 - - - +
404A GLN* 3.5 8.4 + - - +
414A GLU* 4.0 30.9 + - - +
415A LEU* 2.7 46.3 + - + +
416A GLN* 4.0 5.3 - - - +
417A LEU* 3.7 32.8 - - + +
1041A ARG* 3.0 18.4 + - - -
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Residues in contact with ARG 332 (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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328A ASP* 3.0 47.0 + - - +
331A ARG* 1.3 83.7 - - + +
333A TYR* 1.3 113.3 + - + +
402A LEU* 4.4 11.0 + - - +
404A GLN* 3.3 38.9 - - + +
1032A LEU* 4.9 9.7 - - - +
1041A ARG* 3.0 24.5 + - - +
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Residues in contact with TYR 333 (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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329A TYR* 2.9 53.2 + + + +
332A ARG* 1.3 125.1 + - + +
334A THR* 1.3 59.8 + - - +
402A LEU* 3.9 21.3 - - + -
1028A ASN 4.1 4.9 - - - -
1029A VAL* 2.8 51.7 + - + +
1032A LEU* 4.3 6.9 - - + +
1035A TRP* 3.6 12.4 - + + -
1041A ARG* 3.3 7.7 - - - +
1042A GLN* 2.9 43.8 + - - +
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Residues in contact with THR 334 (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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329A TYR* 4.6 1.1 - - + +
330A VAL* 2.5 37.8 + - + -
333A TYR* 1.3 83.2 - - - +
335A ASP* 1.3 59.3 + - - +
336A MET* 3.2 23.7 + - - +
337A PRO* 3.6 4.2 - - - +
562A ILE* 3.4 33.2 - - + -
1041A ARG* 2.9 31.7 + - - -
1042A GLN* 3.6 13.7 - - + +
1044A LEU* 4.0 9.6 - - + -
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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