Contacts of the helix formed by residues 331 - 343 (chain A) in PDB entry 1EZW
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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ASP* 5.3 0.2 + - - -
329A GLY 3.9 1.6 - - - -
330A PRO* 1.3 79.1 - - + +
332A LYS* 1.3 59.2 + - - +
333A GLU* 3.2 11.1 + - - +
334A LYS* 2.8 60.7 + - + +
335A ALA* 2.9 29.8 + - - +
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.4 8.3 - - + -
22A LEU* 4.0 28.5 - - + -
326A SER* 5.0 7.0 + - - +
327A PRO* 3.3 33.6 + - - +
328A ILE* 4.1 24.5 - - + -
329A GLY 3.9 4.1 + - - +
330A PRO 4.0 0.6 + - - -
331A ASP* 1.3 72.4 + - - +
333A GLU* 1.3 57.6 + - - +
335A ALA* 3.3 6.8 + - - +
336A ILE* 2.9 36.3 + - + +
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Residues in contact with GLU 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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18A LYS* 5.9 0.7 - - - -
21A HIS* 2.7 36.9 + - - -
22A LEU* 3.8 16.8 - - + +
25A VAL* 4.3 17.8 - - + +
331A ASP* 3.2 7.0 + - - +
332A LYS* 1.3 78.4 - - - +
334A LYS* 1.3 64.5 + - + +
336A ILE* 3.3 6.3 + - - +
337A GLU* 3.1 37.8 + - - +
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Residues in contact with LYS 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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235A ASP* 4.3 15.3 + - - -
236A LYS* 4.5 16.7 - - - +
240A LYS* 5.8 3.4 - - - +
330A PRO* 5.7 1.6 - - - +
331A ASP* 2.8 46.2 + - - +
333A GLU* 1.3 77.5 - - + +
335A ALA* 1.3 58.1 + - - +
337A GLU* 3.3 15.3 + - - +
338A LEU* 2.9 29.8 + - - +
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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
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234A ILE* 3.6 17.1 - - + +
328A ILE* 3.5 32.3 - - + +
329A GLY* 3.7 11.4 - - - -
331A ASP 2.9 18.0 + - - +
332A LYS 3.5 5.2 - - - +
334A LYS* 1.3 75.3 - - - +
336A ILE* 1.3 65.6 + - - +
338A LEU* 3.2 4.7 + - - +
339A VAL* 2.9 27.8 + - - +
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Residues in contact with ILE 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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8A ILE* 3.5 31.4 - - + -
22A LEU* 3.9 34.8 - - + +
25A VAL* 3.8 11.7 - - + +
26A ALA* 3.5 31.4 - - + +
29A ASN* 4.1 3.3 - - + +
31A PHE* 3.8 15.8 - - + -
324A VAL* 5.9 0.4 - - + -
328A ILE* 4.0 12.3 - - + -
332A LYS* 2.9 25.2 + - + +
333A GLU* 3.6 5.2 - - - +
335A ALA* 1.3 75.6 - - - +
337A GLU* 1.3 58.6 + - - +
339A VAL* 3.3 9.7 + - - +
340A GLY* 3.0 22.9 + - - -
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Residues in contact with GLU 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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25A VAL* 3.9 9.9 - - + +
29A ASN* 3.5 26.9 + - - +
333A GLU* 3.1 31.7 + - - +
334A LYS* 3.6 17.0 - - - +
336A ILE* 1.3 74.6 - - - +
338A LEU* 1.3 60.6 + - - +
340A GLY 3.2 0.3 + - - -
341A GLN* 2.8 38.7 + - + +
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Residues in contact with LEU 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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234A ILE* 4.0 9.6 - - + +
235A ASP* 3.6 18.8 - - - +
236A LYS* 3.6 33.4 - - + +
304A PRO* 3.8 17.9 - - + -
334A LYS 2.9 17.7 + - - +
335A ALA* 3.2 7.4 + - - +
337A GLU* 1.3 74.6 - - - +
339A VAL* 1.3 58.4 + - - +
341A GLN* 4.7 2.7 - - + -
342A GLU* 2.8 65.7 + - + +
343A VAL* 3.7 1.4 + - - +
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Residues in contact with VAL 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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6A PHE* 4.3 10.8 - - + -
31A PHE* 3.6 27.6 - - + -
232A PHE* 3.7 33.4 - - + -
234A ILE* 3.9 8.1 - - + -
324A VAL* 4.7 4.9 - - + -
328A ILE* 6.3 0.4 - - + -
335A ALA 2.9 18.9 + - - +
336A ILE* 3.5 7.9 - - - +
338A LEU* 1.3 77.1 - - - +
340A GLY* 1.3 60.3 + - - +
343A VAL* 3.0 19.9 + - + -
344A ILE* 2.9 44.8 + - + -
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Residues in contact with GLY 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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29A ASN* 3.3 37.2 - - - +
336A ILE 3.0 11.9 + - - -
337A GLU 3.2 2.9 + - - -
339A VAL* 1.3 77.4 - - - +
341A GLN* 1.3 61.9 + - - +
344A ILE* 4.2 6.7 - - - +
345A PRO* 3.2 23.6 - - - +
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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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29A ASN* 4.7 6.8 - - - +
337A GLU* 2.8 23.1 + - + +
338A LEU* 4.2 2.7 - - + +
340A GLY* 1.3 81.6 - - - +
342A GLU* 1.3 70.9 + - + +
343A VAL 3.8 0.4 - - - -
345A PRO* 3.7 14.4 - - - +
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Residues in contact with GLU 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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304A PRO* 3.3 31.3 - - + +
308A VAL* 3.7 5.0 - - - +
338A LEU* 2.8 37.8 + - + +
341A GLN* 1.3 84.4 - - + +
343A VAL* 1.3 63.7 + - - +
345A PRO* 4.3 1.1 - - - -
346A HIS* 3.0 27.7 + - - +
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Residues in contact with VAL 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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6A PHE* 4.1 10.3 - - + -
234A ILE* 3.6 31.9 - - + -
304A PRO* 4.5 4.3 - - + -
307A VAL* 4.0 10.3 - - + -
308A VAL* 3.9 11.9 - - + -
311A ILE* 3.6 31.0 - - + -
338A LEU 4.2 0.4 - - - +
339A VAL* 3.0 20.6 + - + +
342A GLU* 1.3 83.5 - - - +
344A ILE* 1.3 69.0 + - - +
345A PRO* 3.3 2.1 - - - +
346A HIS* 3.0 15.6 + - - +
347A PHE* 3.2 23.2 - - + -
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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