Contacts of the helix formed by residues 323 - 337 (chain B) in PDB entry 4U7D
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 SER 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B CYS* 4.0 1.6 - - - +
322B PHE* 1.3 93.4 - - - +
324B GLN* 1.3 66.1 + - - +
325B LYS* 3.8 8.2 + - - +
326B ASP* 3.2 31.0 + - - +
327B SER* 3.3 16.3 + - - -
371B THR* 3.4 16.2 - - - +
425B ARG* 4.1 2.3 + - - -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B SER* 1.3 72.6 - - - +
325B LYS* 1.3 70.9 + - + +
327B SER* 3.0 17.8 + - - -
328B GLU* 3.1 21.1 + - - +
345B HIS* 3.2 39.9 - - + -
347B ASN* 2.8 34.2 + - - +
371B THR* 3.8 10.9 - - + +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B SER* 3.2 7.9 + - - +
324B GLN* 1.3 85.7 - - + +
326B ASP* 1.3 63.1 + - - +
328B GLU* 3.3 10.0 + - + +
329B GLN* 2.9 56.2 + - + +
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Residues in contact with ASP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B CYS* 3.7 15.3 - - + -
322B PHE* 3.6 9.4 + - - +
323B SER* 3.2 25.9 + - - +
325B LYS* 1.3 82.1 - - - +
327B SER* 1.3 59.9 + - - +
329B GLN* 3.9 12.1 - - - +
330B VAL* 3.0 33.1 + - - +
389B HIS* 4.1 13.0 + - + +
390B SER* 3.9 4.0 + - - -
425B ARG* 2.7 36.8 + - - -
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Residues in contact with SER 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B CYS* 4.1 7.4 - - - +
323B SER 3.3 9.2 + - - -
324B GLN* 3.0 12.3 + - - -
325B LYS 3.1 1.0 - - - -
326B ASP* 1.3 81.3 - - - +
328B GLU* 1.3 56.7 + - - +
331B THR* 2.4 39.5 + - - -
343B ALA* 3.9 7.2 - - - +
344B TYR 4.6 1.0 + - - -
345B HIS* 3.5 17.9 - - - -
369B VAL* 3.6 30.3 + - - +
370B ALA* 4.6 5.8 - - - -
371B THR* 4.7 3.1 - - - -
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLN* 3.1 24.5 + - - +
325B LYS* 3.8 9.2 - - + +
327B SER* 1.3 83.3 + - - +
329B GLN* 1.3 64.0 + - + +
331B THR* 3.8 5.1 - - - -
332B VAL* 3.3 27.5 + - - +
343B ALA* 4.9 6.5 - - + -
345B HIS* 3.2 28.7 + - + +
348B LEU* 5.6 0.6 - - + +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS* 2.9 43.0 + - + +
326B ASP* 3.9 13.6 - - - +
328B GLU* 1.3 79.3 - - + +
330B VAL* 1.3 61.1 + - + +
332B VAL* 3.6 5.3 - - - +
333B SER* 2.9 32.9 + - - +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 4.1 16.2 - - + -
304B ILE* 5.4 2.7 - - + -
319B ILE* 5.0 6.1 - - + -
321B CYS* 4.5 3.4 - - - -
326B ASP* 3.0 20.7 + - - +
327B SER 4.2 1.6 - - - +
329B GLN* 1.3 75.4 - - + +
331B THR* 1.3 65.7 + - - +
333B SER* 3.4 7.0 - - - -
334B LEU* 3.0 39.8 + - + +
369B VAL* 4.2 14.8 - - + -
389B HIS* 3.7 38.1 - - + +
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Residues in contact with THR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B SER 2.4 27.2 + - - -
328B GLU* 3.8 4.9 - - - -
330B VAL* 1.3 75.6 - - - +
332B VAL* 1.3 65.5 + - + +
334B LEU* 3.0 5.0 + - - +
335B GLN* 2.8 37.0 + - - +
341B ALA* 3.5 33.4 - - + +
342B GLY* 4.1 0.4 - - - -
343B ALA* 3.4 28.5 - - + +
369B VAL* 3.6 16.4 - - + +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU 3.3 12.5 + - - +
329B GLN* 3.6 10.1 - - - +
331B THR* 1.3 79.3 - - + +
333B SER* 1.3 66.5 + - - +
335B GLN* 3.1 16.3 + - - +
336B ASN* 3.0 42.5 + - - +
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.7 30.8 - - - +
329B GLN* 2.9 17.5 + - - +
330B VAL* 3.4 9.5 - - - -
332B VAL* 1.3 80.2 - - - +
334B LEU* 1.3 61.2 + - - +
336B ASN* 3.7 8.7 + - - +
337B LEU* 3.5 25.3 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 4.5 12.1 - - + -
304B ILE* 4.0 17.7 - - + -
305B VAL* 3.8 27.1 - - + -
308B ILE* 5.0 1.8 - - + -
319B ILE* 4.0 21.8 - - + -
330B VAL* 3.0 32.2 + - + +
331B THR 3.0 6.2 + - - +
333B SER* 1.3 73.1 - - - +
335B GLN* 1.3 66.4 + - - +
336B ASN 3.2 0.4 - - - -
337B LEU* 3.0 14.7 + - - +
338B GLY 3.3 0.2 + - - -
339B ILE* 3.1 39.9 + - + +
341B ALA* 4.0 19.5 - - + -
367B VAL* 5.6 0.4 - - + -
369B VAL* 4.1 4.3 - - + -
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Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 2.8 28.0 + - - +
332B VAL* 3.4 19.5 - - - +
334B LEU* 1.3 76.7 - - - +
336B ASN* 1.3 63.9 + - - +
338B GLY* 3.1 15.4 + - - -
339B ILE 3.6 13.9 - - - +
341B ALA* 3.0 29.4 + - + +
342B GLY* 5.0 0.8 - - - -
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Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 3.0 37.4 + - - +
333B SER* 3.7 9.8 - - - +
334B LEU 3.2 0.2 - - - -
335B GLN* 1.3 78.0 - - - +
337B LEU* 1.3 67.1 + - + +
338B GLY 3.4 1.7 + - - -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.5 33.4 - - + +
302B GLU* 5.2 8.5 - - + +
305B VAL* 3.7 33.4 - - + +
309B ASN* 4.9 2.9 + - - -
333B SER 3.5 10.9 + - - +
334B LEU 3.0 9.7 + - - +
336B ASN* 1.3 84.5 - - + +
338B GLY* 1.3 56.9 + - - +
339B ILE* 3.5 5.0 + - + +
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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