Contacts of the helix formed by residues 332 - 343 (chain A) in PDB entry 4X4W
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 ALA 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PHE* 4.0 11.1 - - + -
324A ILE* 4.3 19.1 - - + +
327A SER* 3.3 29.8 - - - +
331A ASP* 1.3 77.1 - - - +
333A THR* 1.3 58.7 + - - +
335A ARG* 3.3 17.4 + - - +
336A VAL* 2.8 33.3 + - - +
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Residues in contact with THR 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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324A ILE* 3.6 33.9 - - + +
331A ASP 3.3 0.6 - - - -
332A ALA* 1.3 78.7 - - - +
334A THR* 1.3 58.0 + - - +
336A VAL* 3.3 1.4 + - - +
337A CYS* 2.9 43.7 + - - -
352A MET* 4.5 11.7 - - + +
353A GLN* 5.5 3.4 - - - +
355A TRP* 5.8 2.5 - - + +
357A ILE* 4.0 16.1 - - + +
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Residues in contact with THR 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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265A LYS* 3.6 31.6 - - + -
292A GLU* 4.5 8.7 - - - +
296A LEU* 5.9 1.8 - - + -
331A ASP* 3.4 21.1 + - - +
332A ALA 3.3 0.4 - - - -
333A THR* 1.3 79.2 - - - +
335A ARG* 1.3 59.0 + - + +
337A CYS* 3.3 7.1 + - - +
338A GLU* 3.0 30.5 + - + +
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Residues in contact with ARG 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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295A ASN* 4.4 17.0 + - - +
296A LEU* 4.0 25.5 - - + +
299A PHE* 3.4 55.2 - - + +
323A PHE* 4.4 8.3 - - - -
327A SER 3.8 14.8 + - - -
331A ASP* 3.3 30.7 + - - +
332A ALA* 3.3 26.2 + - - +
333A THR 3.2 0.4 - - - -
334A THR* 1.3 79.5 - - + +
336A VAL* 1.3 63.1 + - - +
338A GLU* 3.3 4.0 + - - +
339A LEU 3.0 18.0 + - - -
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Residues in contact with VAL 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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299A PHE* 4.2 11.9 - - + -
307A LEU* 4.7 6.7 - - + -
320A TYR* 3.9 33.7 - - + +
323A PHE* 3.7 27.4 - - + -
324A ILE* 3.9 13.0 - - + -
332A ALA 2.8 21.0 + - - +
333A THR 3.8 3.1 - - - +
335A ARG* 1.3 77.2 - - - +
337A CYS* 1.3 63.0 + - - +
339A LEU* 3.1 5.2 + - - +
340A LEU* 2.9 22.5 + - + +
352A MET* 4.1 20.2 - - + -
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Residues in contact with CYS 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 THR* 2.9 30.3 + - - +
334A THR* 3.7 5.8 - - - +
336A VAL* 1.3 74.6 - - - +
338A GLU* 1.3 67.3 + - - +
340A LEU* 3.2 4.4 + - - -
341A LYS* 3.0 28.1 + - - +
349A LEU* 3.5 17.0 - - + +
352A MET* 3.6 25.6 - - - -
353A GLN* 3.6 32.5 - - + +
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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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264A PRO* 3.7 4.2 - - - +
265A LYS* 2.8 46.9 + - + +
268A THR* 2.6 41.9 + - + +
296A LEU* 3.9 20.0 - - + -
300A ILE* 4.7 2.0 - - + -
334A THR* 3.0 19.8 + - + +
335A ARG 3.8 6.5 - - - +
337A CYS* 1.3 76.6 - - - +
339A LEU* 1.3 57.9 + - - +
341A LYS* 2.8 35.9 + - - +
342A TYR* 2.8 25.1 + - - +
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Residues in contact with LEU 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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299A PHE* 3.9 15.5 - - + -
300A ILE* 4.5 15.8 - - + +
303A ASN* 4.2 7.0 - - + +
304A ARG* 3.8 29.4 - - + +
307A LEU* 3.9 46.0 - - + +
320A TYR* 4.2 6.3 - - + -
335A ARG 3.0 13.1 + - - +
336A VAL* 3.1 8.9 + - - +
338A GLU* 1.3 76.3 - - - +
340A LEU* 1.3 57.4 + - - +
342A TYR* 3.1 10.3 + - + +
343A GLN* 2.9 44.3 + - + +
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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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317A LEU* 4.3 5.4 - - + -
320A TYR* 3.4 42.4 - - + +
336A VAL* 2.9 22.5 + - + +
337A CYS* 3.6 9.4 - - - +
339A LEU* 1.3 75.4 - - - +
341A LYS* 1.3 62.4 + - - +
343A GLN* 3.4 3.5 + - - -
344A GLY 3.1 2.9 + - - -
345A GLU* 3.0 47.6 + - + +
348A LEU* 3.8 17.5 - - + +
349A LEU* 4.0 16.2 - - + -
352A MET* 3.6 34.3 - - + -
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Residues in contact with LYS 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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258A ASN* 3.5 9.5 - - - +
259A VAL* 3.5 24.7 - - + +
262A PHE* 3.2 24.3 + - + +
263A SER* 2.9 24.2 + - - -
264A PRO* 4.1 7.4 - - + -
268A THR* 4.7 1.8 - - + -
337A CYS* 3.0 18.6 + - - +
338A GLU* 2.8 43.1 + - - +
340A LEU* 1.3 74.1 - - - +
342A TYR* 1.3 66.5 + - - +
344A GLY* 2.9 13.0 + - - -
346A HIS* 6.0 2.9 - - - -
349A LEU* 3.7 31.0 - - + -
353A GLN* 4.4 11.8 - - - +
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Residues in contact with TYR 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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251A GLU* 2.6 28.9 + - - -
255A VAL* 3.6 23.4 - - + +
258A ASN* 2.9 21.8 + - - +
259A VAL* 4.0 9.8 - - - +
268A THR* 3.3 24.4 - - + +
271A ALA 4.0 0.4 - - - -
272A SER* 3.4 30.6 - - - -
300A ILE* 3.6 17.9 - - + -
304A ARG* 2.9 50.9 + - + -
338A GLU 2.8 16.1 + - - +
339A LEU* 3.1 13.7 + - + +
341A LYS* 1.3 71.7 - - - +
343A GLN* 1.3 65.4 + - + +
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Residues in contact with GLN 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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258A ASN* 3.4 9.7 + - - +
304A ARG 3.1 25.0 + - - +
307A LEU 2.9 23.2 + - - -
308A ILE* 3.8 8.8 - - - +
320A TYR* 2.6 31.8 + - - -
339A LEU* 2.9 38.8 + - + +
340A LEU* 4.0 6.0 - - - +
342A TYR* 1.3 82.1 - - + +
344A GLY* 1.3 63.6 + - - +
345A GLU* 3.5 15.1 + - + +
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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