Contacts of the helix formed by residues 322 - 334 (chain A) in PDB entry 2CW9
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 ASP 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A GLN* 2.9 35.9 + - + +
320A GLU 3.5 1.0 - - - -
321A ASN* 1.3 81.7 - - + +
323A ILE* 1.3 69.6 + - - +
324A ILE 3.6 0.9 - - - -
325A PRO* 3.5 2.3 - - - +
326A ASN* 2.9 52.4 + - - +
342A TRP* 3.8 18.1 - - - -
435A TYR 4.6 4.5 - - - +
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Residues in contact with ILE 323 (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 PHE* 4.8 1.3 - - + -
318A GLN* 3.2 28.2 + - + +
319A CYS* 4.0 24.7 - - + -
322A ASP* 1.3 80.9 - - - +
324A ILE* 1.3 66.7 + - + +
326A ASN* 4.2 0.2 - - - +
327A VAL* 3.1 37.1 + - + +
342A TRP* 4.1 29.4 - - + -
423A TRP* 4.5 6.5 - - + -
425A LEU* 4.1 27.8 - - + -
438A TRP* 4.2 27.4 - - + +
439A ARG 6.3 0.2 - - - -
440A LEU 6.1 0.4 - - - +
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Residues in contact with ILE 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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319A CYS* 2.9 32.9 + - + +
320A GLU* 4.4 2.2 - - - -
323A ILE* 1.3 72.3 - - + +
325A PRO* 1.3 60.3 - - + +
328A LEU* 2.9 37.5 + - + +
372A ILE* 3.7 24.5 - - + -
375A VAL* 4.1 20.4 - - + -
391A ILE* 4.0 18.2 - - + -
393A PHE* 3.6 55.2 - - + -
423A TRP* 3.9 13.9 - - + -
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Residues in contact with PRO 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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319A CYS 3.6 2.2 - - - +
320A GLU 3.1 26.0 - - - +
321A ASN* 4.2 10.1 - - - +
322A ASP 3.5 12.3 - - - +
324A ILE* 1.3 94.5 - - + +
326A ASN* 1.3 63.6 + - - +
328A LEU* 4.3 1.0 - - + +
329A GLU* 3.1 27.5 + - - +
369A ILE* 4.5 4.4 - - + +
372A ILE* 4.2 20.4 - - + -
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Residues in contact with ASN 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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321A ASN 5.2 0.8 + - - -
322A ASP* 2.9 44.1 + - - +
325A PRO* 1.3 80.5 - - - +
327A VAL* 1.3 63.9 + - - +
329A GLU* 3.9 3.5 - - - +
330A ALA* 3.2 23.4 + - - +
338A ILE* 4.7 4.7 - - + +
342A TRP* 4.0 25.1 - - + +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 3.1 25.7 + - + +
326A ASN* 1.3 74.0 - - - +
328A LEU* 1.3 65.1 + - - +
330A ALA* 3.2 6.6 + - - +
331A MSE 3.0 35.7 + - + +
339A LEU* 4.4 8.9 - - + +
342A TRP* 3.6 44.2 - - + +
423A TRP* 3.5 23.6 - - + -
440A LEU* 4.2 24.9 - - + +
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Residues in contact with LEU 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 ILE 2.9 18.9 + - - +
327A VAL* 1.3 76.3 - - - +
329A GLU* 1.3 63.0 + - - +
331A MSE 3.3 15.2 + - + +
332A ILE* 3.1 38.6 + - + +
369A ILE* 3.8 21.3 - - + -
372A ILE* 4.3 11.9 - - + -
393A PHE* 4.2 22.0 - - + -
395A ALA* 4.4 7.6 - - + -
397A LEU* 4.2 15.7 - - + -
421A TYR* 4.1 21.8 - - + +
423A TRP* 3.9 17.0 - - + -
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Residues in contact with GLU 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 PRO 3.1 22.2 + - - +
326A ASN* 3.9 4.9 - - - +
328A LEU* 1.3 78.5 - - - +
330A ALA* 1.3 62.4 + - - +
332A ILE* 3.5 11.0 + - - +
333A SER* 2.7 54.3 + - - +
335A GLU* 4.3 8.7 - - - +
367A SER 4.6 4.3 - - - +
368A ARG* 5.5 1.7 - - - +
369A ILE* 3.9 21.2 + - + +
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Residues in contact with ALA 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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326A ASN 3.2 16.2 + - - +
327A VAL* 3.2 6.0 + - - +
329A GLU* 1.3 78.6 - - - +
331A MSE 1.3 63.8 + - - +
334A GLY* 3.1 3.8 + - - -
335A GLU* 3.0 55.7 + - - +
338A ILE* 3.8 21.5 - - + -
339A LEU* 4.4 14.0 - - + +
342A TRP* 5.8 0.2 - - + -
355A ILE* 5.1 0.2 - - - +
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Residues in contact with MSE 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 VAL* 3.0 31.2 + - + +
328A LEU* 3.5 16.6 - - + +
330A ALA* 1.3 79.2 - - - +
332A ILE* 1.3 64.8 + - + +
333A SER 3.5 0.2 + - - -
334A GLY* 3.6 5.4 + - - -
339A LEU* 3.8 26.0 - - + -
351A LEU* 4.3 20.2 - - + -
355A ILE* 4.0 14.0 - - - +
365A PHE* 5.8 1.4 - - - -
421A TYR* 5.4 3.4 - - + +
423A TRP* 4.3 10.1 - - - -
440A LEU* 4.8 2.9 - - - -
443A ILE* 3.9 22.9 - - + -
1001A 1PE 3.6 34.1 - - - +
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Residues in contact with ILE 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 LEU* 3.1 28.9 + - + +
329A GLU* 3.5 9.6 - - - +
331A MSE 1.3 79.8 - - + +
333A SER* 1.3 65.5 + - - +
334A GLY 3.3 0.4 - - - -
365A PHE* 3.6 20.6 - - - +
367A SER* 3.9 45.1 + - - +
368A ARG* 4.0 6.5 - - - +
369A ILE* 3.7 31.0 - - + -
397A LEU* 4.4 8.5 - - + -
399A MSE 4.0 25.7 - - + +
421A TYR* 5.7 0.4 - - - +
1001A 1PE 4.8 4.7 - - - +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 2.7 39.2 + - - -
332A ILE* 1.3 78.4 - - - +
334A GLY* 1.3 64.6 + - - +
335A GLU* 3.4 22.8 + - - +
359A LYS* 5.2 0.7 + - - -
365A PHE* 3.6 23.8 + - - +
367A SER 4.4 5.9 + - - -
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Residues in contact with GLY 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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330A ALA 3.1 5.6 + - - -
331A MSE 3.6 2.2 + - - -
332A ILE 3.3 3.6 - - - -
333A SER* 1.3 79.7 - - - +
335A GLU* 1.3 59.0 + - - +
336A LEU* 3.2 7.2 + - - -
355A ILE* 3.9 29.6 - - - +
359A LYS* 3.1 28.2 + - - -
365A PHE* 3.9 12.2 - - - -
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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