Contacts of the helix formed by residues 333 - 348 (chain A) in PDB entry 2YHS
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 ARG 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A ASN* 3.4 41.9 - - - +
307A THR* 5.8 1.6 + - - -
330A ASP* 3.2 30.6 + - - +
331A THR 4.9 0.4 - - - -
332A PHE* 1.3 81.1 - - + +
334A ALA* 1.3 66.3 + - - +
335A ALA* 3.1 23.0 - - + +
336A ALA* 3.0 28.8 + - + +
337A VAL* 3.1 11.0 + - - +
386A ARG* 3.3 54.4 - - + +
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Residues in contact with ALA 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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332A PHE 3.8 4.2 + - - -
333A ARG* 1.3 72.2 - - - +
335A ALA* 1.3 57.7 + - - +
337A VAL* 3.3 7.1 + - - +
338A GLU* 2.8 34.3 + - - +
356A THR* 3.6 26.9 - - + +
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 3.1 16.3 - - - +
334A ALA* 1.3 78.9 - - - +
336A ALA* 1.3 57.5 + - - +
338A GLU* 4.0 9.9 - - - +
339A GLN* 3.0 30.3 + - - +
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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
----------------------------------------------------------
307A THR* 5.6 5.6 - - - +
330A ASP* 3.7 22.7 - - + +
333A ARG* 3.0 37.4 + - - +
335A ALA* 1.3 75.9 - - - +
337A VAL* 1.3 65.1 + - - +
339A GLN* 3.5 7.5 + - - +
340A LEU* 3.3 27.9 + - - +
382A ASP* 4.6 7.4 - - - +
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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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328A ALA* 4.0 20.0 - - + +
330A ASP* 3.3 30.3 - - + +
331A THR* 4.2 9.6 - - + +
333A ARG 3.1 8.1 + - - +
334A ALA* 3.8 8.7 - - - +
336A ALA* 1.3 73.9 - - - +
338A GLU* 1.3 65.8 + - - +
340A LEU* 3.3 4.0 + - - +
341A GLN* 3.0 38.0 + - - +
353A ALA* 3.8 21.3 - - + -
354A GLN 4.4 13.5 - - - +
356A THR* 6.1 1.1 - - - +
1497A EDO 4.6 2.9 - - - +
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Residues in contact with GLU 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 ALA 2.8 20.0 + - - +
335A ALA* 4.0 8.6 - - - +
337A VAL* 1.3 73.4 - - - +
339A GLN* 1.3 64.4 + - - +
341A GLN* 4.3 10.3 - - - +
342A VAL* 2.9 47.3 + - + +
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Residues in contact with GLN 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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307A THR* 3.9 20.5 - - + +
335A ALA 3.0 19.8 + - - +
336A ALA* 3.5 10.3 - - - +
337A VAL 3.2 0.4 - - - -
338A GLU* 1.3 82.5 + - - +
340A LEU* 1.3 60.7 + - - +
342A VAL* 4.3 2.2 - - - +
343A TRP* 3.1 25.1 + - - +
1496A EDO 3.0 25.2 + - - +
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Residues in contact with LEU 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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307A THR* 4.3 13.5 - - + -
310A ILE* 4.4 16.2 - - + -
326A LEU* 4.2 24.5 - - + +
327A ALA 4.4 3.1 - - - +
328A ALA* 4.0 20.9 - - + +
336A ALA 3.3 10.3 + - - +
337A VAL 3.3 6.7 + - - +
339A GLN* 1.3 74.3 - - - +
341A GLN* 1.3 61.2 + - - +
343A TRP* 3.8 2.6 - - + +
344A GLY 2.8 25.8 + - - -
351A VAL* 3.4 19.9 - - + +
380A ILE 6.1 0.2 - - - +
382A ASP* 3.9 34.1 - - + +
1496A EDO 4.1 20.4 - - - -
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Residues in contact with GLN 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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337A VAL* 3.0 25.5 + - - +
338A GLU* 3.3 10.0 + - - +
340A LEU* 1.3 79.0 - - - +
342A VAL* 1.3 59.3 + - + +
344A GLY* 3.8 0.7 - - - -
345A GLN* 3.0 29.8 + - - +
351A VAL* 4.0 21.2 + - + +
353A ALA* 3.5 25.9 + - + +
1497A EDO 3.2 42.0 + - - -
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Residues in contact with VAL 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 GLU* 2.9 40.3 + - + +
339A GLN* 4.3 2.5 - - - +
341A GLN* 1.3 73.9 - - + +
343A TRP* 1.3 66.9 + - - +
345A GLN* 3.2 14.7 + - + +
346A ARG* 2.9 26.8 + - + +
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Residues in contact with TRP 343 (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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311A GLY* 3.8 32.3 - - - -
314A ALA* 4.0 7.0 - - + -
315A ARG* 4.0 11.7 - - + -
326A LEU* 4.0 26.9 - - + -
339A GLN 3.1 18.8 + - - +
340A LEU 3.8 2.2 - - - +
342A VAL* 1.3 80.0 - - - +
344A GLY* 1.3 66.7 + - - +
346A ARG* 3.2 2.7 + - - -
347A ASN* 2.9 61.2 + - + +
349A ILE* 3.6 34.3 - - + -
1496A EDO 3.6 35.7 - - - +
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Residues in contact with GLY 344 (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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340A LEU 2.8 21.1 + - - -
343A TRP* 1.3 82.8 - - - +
345A GLN* 1.3 56.8 + - - +
347A ASN 3.2 0.3 + - - -
348A ASN 2.8 27.0 + - - -
349A ILE* 2.8 32.3 + - - -
351A VAL* 3.7 9.0 - - - -
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Residues in contact with GLN 345 (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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341A GLN 3.0 17.4 + - - +
342A VAL* 3.5 14.7 - - - +
344A GLY* 1.3 76.4 - - - +
346A ARG* 1.3 61.6 + - - +
347A ASN 3.3 0.2 + - - -
348A ASN* 3.4 14.6 + - - +
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Residues in contact with ARG 346 (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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342A VAL* 2.9 19.5 + - + +
343A TRP* 3.8 4.7 - - - +
345A GLN* 1.3 76.0 - - - +
347A ASN* 1.3 70.6 + - - +
348A ASN* 3.4 4.9 + - - -
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Residues in contact with ASN 347 (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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315A ARG* 4.2 14.2 + - - +
318A GLU* 4.5 5.4 - - - +
343A TRP* 2.9 76.3 + - + +
344A GLY 4.2 0.7 - - - +
346A ARG* 1.3 92.2 - - - +
348A ASN* 1.3 69.9 + - - +
349A ILE* 3.3 14.0 + - + +
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Residues in contact with ASN 348 (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 GLU* 4.5 0.9 - - - +
344A GLY 2.8 7.4 + - - -
345A GLN* 3.4 14.2 + - - +
346A ARG 3.4 4.0 + - - -
347A ASN* 1.3 82.1 - - - +
349A ILE* 1.3 57.2 + - - +
350A PRO* 4.2 1.1 - - - +
1498A EDO 3.5 18.4 - - - -
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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