Contacts of the helix formed by residues 332 - 343 (chain A) in PDB entry 1CEZ
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 LYS 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A ILE* 3.1 9.0 + - - +
331A ASN* 1.3 70.9 + - - +
333A LYS* 1.3 65.7 + - + +
335A LEU* 3.2 9.6 + - + +
336A ALA* 2.8 26.0 + - - +
409A ALA* 3.0 35.9 - - + +
410A ASN* 2.7 28.8 - - - +
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Residues in contact with LYS 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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331A ASN* 3.2 8.5 + - - +
332A LYS* 1.3 79.0 - - + +
334A VAL* 1.3 62.5 + - - +
336A ALA* 3.4 7.7 + - - +
337A VAL* 3.4 18.0 + - - +
516A PHE* 3.3 62.9 + - + +
517A GLU* 4.6 9.3 + - - -
528A TYR* 5.0 6.1 + - - -
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Residues in contact with VAL 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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331A ASN* 3.2 21.0 + - - +
333A LYS* 1.3 72.8 - - - +
335A LEU* 1.3 60.6 + - - +
337A VAL* 3.0 6.9 + - - +
338A ALA* 2.8 26.7 + - - +
442A GLY* 3.6 35.4 - - - +
443A LEU* 4.1 7.2 - - + -
509A PHE* 4.0 28.3 - - + +
512A LEU* 4.7 4.0 - - + -
513A ALA* 3.8 28.5 - - + +
516A PHE* 4.2 11.2 - - + -
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Residues in contact with LEU 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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330A ILE* 3.6 17.3 - - + -
331A ASN 3.0 12.8 + - - +
332A LYS* 3.4 12.1 - - + +
334A VAL* 1.3 77.1 - - - +
336A ALA* 1.3 58.7 + - - +
338A ALA* 3.2 0.8 + - - -
339A ASN* 2.7 68.8 + - - +
402A LEU* 5.2 2.5 - - + -
405A ALA* 3.6 19.3 - - + +
406A ASN* 3.0 14.1 - - - +
409A ALA* 3.5 31.6 - - + -
443A LEU* 3.6 14.3 - - + +
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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
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332A LYS 2.8 16.3 + - - +
333A LYS* 3.6 7.9 - - - +
334A VAL 3.2 0.2 - - - -
335A LEU* 1.3 79.2 - - - +
337A VAL* 1.3 62.5 + - + +
339A ASN* 3.9 6.5 + - - +
340A VAL* 3.5 24.3 + - - +
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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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333A LYS 3.4 10.9 + - - +
334A VAL 3.0 7.4 + - - +
336A ALA* 1.3 78.1 - - + +
338A ALA* 1.3 67.0 + - - +
340A VAL* 3.1 2.3 + - - +
341A ILE* 3.0 34.7 + - + +
496A PRO* 3.6 32.8 - - + -
497A LEU* 4.5 13.7 - - + -
502A TRP* 3.7 35.0 - - + -
509A PHE* 4.7 1.8 - - + -
512A LEU* 3.9 12.6 - - + -
516A PHE* 4.6 2.0 - - + -
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Residues in contact with ALA 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 VAL 2.8 15.7 + - - +
335A LEU 3.2 4.5 + - - +
337A VAL* 1.3 79.2 - - - +
339A ASN* 1.3 60.8 + - - +
340A VAL 3.1 1.4 + - - -
341A ILE* 4.4 1.8 - - - -
342A THR* 2.8 32.7 + - - +
402A LEU* 3.8 19.3 - - + -
439A MET* 4.4 8.7 - - - -
443A LEU* 4.2 13.5 - - + -
509A PHE* 4.3 22.0 - - + -
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Residues in contact with ASN 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 LEU* 2.7 40.5 + - - +
336A ALA* 4.0 8.0 - - - +
337A VAL 3.3 0.2 - - - -
338A ALA* 1.3 76.1 - - - +
340A VAL* 1.3 64.4 + - + +
342A THR* 4.1 3.5 + - - -
343A LYS* 3.5 20.8 - - - +
402A LEU* 3.7 14.9 - - - +
406A ASN* 2.9 32.3 + - - +
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Residues in contact with VAL 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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336A ALA 3.5 15.5 + - - +
337A VAL 3.1 6.3 + - - +
338A ALA 3.1 0.6 - - - -
339A ASN* 1.3 84.6 - - + +
341A ILE* 1.3 65.3 + - - +
342A THR 3.4 0.7 - - - -
343A LYS* 3.5 10.1 + - - +
344A TRP* 3.3 41.1 - - + +
497A LEU* 4.5 20.0 - - + -
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Residues in contact with ILE 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 15.6 + - + +
338A ALA* 4.1 4.3 - - - +
340A VAL* 1.3 71.7 - - - +
342A THR* 1.3 62.6 + - + +
343A LYS 3.0 5.6 - - - -
344A TRP* 2.9 64.0 + - + +
347A CYS* 4.0 29.6 - - - +
348A PRO* 4.4 7.9 - - + -
349A VAL* 4.2 3.1 - - + -
497A LEU* 3.8 18.6 - - + -
502A TRP* 3.7 32.1 - - + -
509A PHE* 3.9 18.2 - - + -
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Residues in contact with THR 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 ALA* 2.8 27.9 + - - +
339A ASN 4.1 2.3 + - - -
341A ILE* 1.3 80.0 - - + +
343A LYS* 1.3 63.4 + - - +
344A TRP 3.4 2.0 + - - +
347A CYS* 5.9 0.2 - - - -
352A ILE* 4.4 20.8 - - + +
355A ILE* 4.4 2.3 - - - +
395A ARG* 2.5 37.4 + - - -
398A LEU* 3.9 34.1 - - + -
402A LEU* 3.4 15.5 - - + +
439A MET* 4.4 12.1 - - - -
509A PHE* 5.0 1.6 - - + -
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Residues in contact with LYS 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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254A ILE 3.5 0.6 + - - -
255A ALA 2.7 30.7 + - - -
256A THR 4.1 8.3 - - - +
257A ARG 2.9 34.1 + - - -
258A ALA* 4.4 10.5 - - + +
339A ASN 3.5 20.4 - - - +
340A VAL 3.5 6.3 + - - +
341A ILE 3.0 1.8 - - - -
342A THR* 1.3 90.3 - - - +
344A TRP* 1.3 66.8 + - + +
345A LYS* 3.9 10.0 + - - +
355A ILE* 3.6 12.4 - - - +
395A ARG* 4.2 1.1 - - - +
399A GLU* 3.2 22.6 + - - +
402A LEU* 5.5 2.0 - - + -
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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