Contacts of the helix formed by residues 329 - 342 (chain A) in PDB entry 1RS0
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 ASN 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A TYR* 3.6 9.3 - - - +
290A ALA 2.9 9.6 + - - +
291A THR 3.6 21.2 - - - +
292A TYR* 6.0 0.3 - - - -
293A PRO* 5.2 0.3 - - - +
328A THR* 1.3 72.9 - - - +
330A THR* 1.3 59.5 + - - +
331A LYS* 3.1 17.0 - - - +
332A LYS* 2.8 56.5 - - + +
333A ALA 3.3 14.0 + - - -
369A MET* 3.6 19.6 + - + +
370A GLY* 3.4 18.0 + - - -
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Residues in contact with THR 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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289A TYR* 3.3 34.9 + - + +
328A THR* 3.7 5.6 + - - +
329A ASN* 1.3 70.8 - - - +
331A LYS* 1.3 66.5 + - - +
333A ALA* 3.3 1.8 + - + +
334A LEU* 3.1 25.6 + - + +
361A LEU* 4.0 23.8 - - + -
363A THR* 4.7 4.5 + - + +
365A GLY* 6.0 1.2 - - - -
367A HIS* 3.5 21.9 + - - +
369A MET 4.5 0.2 + - - -
373A PRO* 3.9 20.6 - - + -
417A LEU* 4.3 9.0 - - + -
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Residues in contact with LYS 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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329A ASN* 3.1 9.8 - - - +
330A THR* 1.3 80.3 - - - +
332A LYS* 1.3 63.1 + - + +
334A LEU* 3.3 4.5 + - - +
335A GLN* 3.1 42.1 + - - +
367A HIS* 6.1 0.2 - - - -
369A MET 5.1 0.6 + - - -
370A GLY* 4.7 1.6 - - - -
371A GLY* 3.5 40.7 - - - +
372A ASP 4.1 6.0 + - - +
373A PRO* 3.9 14.9 - - + +
375A THR* 3.3 36.2 + - - +
376A VAL* 3.6 13.4 - - + +
379A GLU* 4.5 2.2 + - - -
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Residues in contact with LYS 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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291A THR 3.9 13.0 - - - +
292A TYR* 4.1 26.5 - - + -
293A PRO* 3.7 21.1 - - + +
329A ASN* 2.8 39.4 - - + +
331A LYS* 1.3 76.0 - - + +
333A ALA* 1.3 57.8 + - - +
335A GLN* 2.7 41.3 + - - +
336A ALA 3.0 9.9 + - - -
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Residues in contact with ALA 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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249A VAL* 3.9 15.2 - - + +
287A VAL* 4.9 2.8 - - + +
289A TYR* 3.5 45.1 - - + -
293A PRO* 3.7 14.2 - - + +
329A ASN 3.3 3.6 + - - -
330A THR* 3.5 10.3 - - + +
332A LYS* 1.3 78.4 - - - +
334A LEU* 1.3 63.0 + - + +
336A ALA* 3.3 15.2 + - - +
337A VAL* 3.5 11.7 + - - +
361A LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 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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249A VAL* 5.5 2.5 - - + -
330A THR* 3.1 15.8 + - + +
331A LYS 3.5 8.3 - - - +
332A LYS 3.0 0.6 - - - -
333A ALA* 1.3 75.9 - - + +
335A GLN* 1.3 60.8 + - - +
337A VAL* 3.2 10.9 + - + +
338A TYR* 3.0 21.0 + - - -
359A ILE* 4.4 26.9 - - + -
361A LEU* 5.4 11.7 - - + -
373A PRO* 3.7 38.6 - - + +
376A VAL* 3.4 20.5 - - + +
377A ILE* 4.0 26.2 - - + -
380A ILE* 4.3 3.0 - - + +
400A VAL* 5.8 1.3 - - + -
417A LEU* 4.3 11.7 - - + -
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Residues in contact with GLN 335 (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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331A LYS* 3.1 37.4 + - - +
332A LYS* 2.7 42.8 + - - +
334A LEU* 1.3 70.7 - - - +
336A ALA* 1.3 58.0 + - - -
338A TYR* 3.2 11.6 + - + +
339A SER* 3.0 30.8 + - - -
376A VAL* 3.8 14.6 - - + -
379A GLU* 4.6 12.8 + - - +
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Residues in contact with ALA 336 (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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287A VAL* 4.7 4.0 - - + -
293A PRO* 4.3 12.3 - - + -
295A ILE* 3.5 30.8 - - + +
332A LYS 3.0 8.8 + - - +
333A ALA 3.4 10.8 - - - +
334A LEU 3.2 0.4 - - - -
335A GLN* 1.3 77.1 - - - +
337A VAL* 1.3 62.7 + - - +
339A SER* 3.5 10.0 + - - -
340A MET* 3.4 26.4 + - - +
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Residues in contact with VAL 337 (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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247A TYR* 3.6 34.1 - - + -
249A VAL* 3.8 26.2 - - + -
287A VAL* 5.1 6.3 - - + -
333A ALA 3.7 13.9 - - - +
334A LEU* 3.2 15.9 + - + +
336A ALA* 1.3 77.7 - - - +
338A TYR* 1.3 64.2 + - - +
340A MET* 3.1 20.6 + - + +
341A MET* 3.3 21.1 + - - +
359A ILE* 3.9 22.9 - - + -
380A ILE* 4.7 1.3 - - + -
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Residues in contact with TYR 338 (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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334A LEU 3.0 13.0 + - - +
335A GLN* 3.3 17.0 - - + +
337A VAL* 1.3 76.7 - - - +
339A SER* 1.3 54.7 + - - +
341A MET* 2.9 12.7 + - - +
342A SER* 2.8 51.1 + - - -
376A VAL* 4.5 5.2 - - + -
379A GLU* 4.0 32.0 + - + +
380A ILE* 3.8 21.1 - - + +
383A LEU* 3.6 39.2 - - + +
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Residues in contact with SER 339 (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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335A GLN 3.0 14.6 + - - -
336A ALA* 3.6 12.3 - - - -
337A VAL 3.3 0.2 - - - -
338A TYR* 1.3 80.3 - - - +
340A MET* 1.3 63.2 + - - +
342A SER* 3.3 25.4 + - - +
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Residues in contact with MET 340 (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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247A TYR* 3.9 23.0 + - + -
285A GLY* 4.1 5.6 - - - -
287A VAL* 3.7 29.8 - - + -
295A ILE* 3.8 14.1 - - + -
297A VAL 3.8 13.2 - - - +
298A LYS* 4.0 15.7 - - + -
299A VAL* 3.7 46.8 - - + +
300A SER* 6.1 0.2 - - - -
336A ALA 3.4 17.7 + - - +
337A VAL* 3.1 13.7 + - + +
339A SER* 1.3 78.2 - - - +
341A MET* 1.3 59.0 + - - +
342A SER 4.5 2.4 - - - +
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Residues in contact with MET 341 (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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247A TYR* 3.5 20.0 - - + +
337A VAL* 3.3 28.5 - - + +
338A TYR* 2.9 7.0 + - - +
340A MET* 1.3 77.0 - - - +
342A SER* 1.3 66.8 + - - +
343A TRP* 3.5 5.7 + - - +
357A HIS* 3.4 31.6 - - + +
359A ILE* 5.5 1.1 - - + -
380A ILE* 3.6 28.5 - - + -
383A LEU* 3.8 18.7 - - + +
384A LEU* 3.2 40.2 - - + +
398A LEU* 4.9 2.2 - - + -
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Residues in contact with SER 342 (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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338A TYR* 2.8 34.6 + - - -
339A SER* 3.3 23.9 + - - +
340A MET 4.5 2.3 - - - +
341A MET* 1.3 78.3 - - - +
343A TRP* 1.3 61.0 + - - +
344A PRO 3.9 2.6 - - - -
383A LEU* 4.0 9.9 - - - +
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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