Contacts of the helix formed by residues 323 - 337 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A CYS* 4.0 1.6 - - - +
322A PHE* 1.3 92.8 - - - +
324A GLN* 1.3 65.9 + - - +
325A LYS* 3.9 7.1 + - - +
326A ASP* 3.2 31.5 + - - +
327A SER* 3.1 17.0 + - - -
371A THR* 3.2 15.8 - - - +
425A ARG* 4.3 3.0 + - - -
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Residues in contact with GLN 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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323A SER* 1.3 73.8 - - - +
325A LYS* 1.3 69.1 + - + +
327A SER* 2.8 22.1 + - - -
328A GLU* 2.9 23.9 + - - +
345A HIS* 3.0 41.1 - - + -
347A ASN* 3.0 31.7 + - - +
371A THR* 3.4 10.6 - - + +
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Residues in contact with LYS 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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323A SER* 3.3 5.9 + - - +
324A GLN* 1.3 86.8 - - + +
326A ASP* 1.3 62.6 + - - +
328A GLU* 3.2 9.1 + - + +
329A GLN* 2.8 68.9 + - + +
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Residues in contact with ASP 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 CYS* 3.6 14.8 - - + -
322A PHE* 4.0 4.0 + - - +
323A SER* 3.2 26.6 + - - +
325A LYS* 1.3 79.2 - - - +
327A SER* 1.3 59.9 + - - +
329A GLN* 4.3 12.7 - - - +
330A VAL* 3.0 34.5 + - - +
389A HIS* 3.9 13.3 + - - +
390A SER* 3.9 8.8 + - - -
425A ARG* 2.8 36.5 + - - -
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A CYS* 4.1 4.9 - - - -
323A SER 3.1 10.8 + - - -
324A GLN* 2.8 12.4 + - - -
325A LYS 3.0 0.6 - - - -
326A ASP* 1.3 79.7 - - - +
328A GLU* 1.3 61.1 + - - +
331A THR* 2.4 35.8 + - - -
343A ALA* 4.0 3.6 - - - +
344A TYR 4.5 1.0 + - - -
345A HIS* 3.5 17.8 - - - +
369A VAL* 3.2 34.5 + - - +
370A ALA* 4.4 8.5 - - - -
371A THR* 4.6 1.6 - - - -
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 2.9 23.5 + - - +
325A LYS* 3.8 8.8 - - + +
327A SER* 1.3 81.7 + - - +
329A GLN* 1.3 63.6 + - + +
331A THR* 3.5 4.6 - - - -
332A VAL* 3.1 30.0 + - + +
343A ALA* 4.4 9.9 - - + -
345A HIS* 2.8 32.9 + - + +
348A LEU* 5.1 2.8 - - + +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 2.8 64.0 + - + +
326A ASP* 3.8 14.5 - - - +
328A GLU* 1.3 72.7 - - + +
330A VAL* 1.3 63.2 + - + +
331A THR 3.2 0.2 + - - -
332A VAL* 3.3 5.6 + - - +
333A SER* 2.8 34.8 + - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 3.8 19.7 - - + -
304A ILE* 5.3 2.7 - - + -
319A ILE* 4.9 8.5 - - + -
321A CYS* 4.4 1.6 - - - -
326A ASP* 3.0 20.4 + - - +
329A GLN* 1.3 77.7 - - + +
331A THR* 1.3 57.7 + - - +
333A SER* 3.3 7.5 + - - -
334A LEU* 2.8 45.3 + - + +
369A VAL* 4.1 14.8 - - + -
389A HIS* 3.5 39.3 - - + +
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Residues in contact with THR 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 SER 2.4 23.9 + - - -
328A GLU 3.5 4.9 - - - -
329A GLN 3.2 0.2 - - - -
330A VAL* 1.3 76.3 - - - +
332A VAL* 1.3 66.2 + - + +
334A LEU* 2.8 5.4 + - - +
335A GLN* 2.7 34.7 + - - +
341A ALA* 3.3 36.3 - - + +
342A GLY* 3.7 9.0 - - - +
343A ALA* 3.4 16.3 - - + +
369A VAL* 3.3 20.1 - - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.1 13.3 + - + +
329A GLN* 3.6 9.0 - - - +
331A THR* 1.3 78.4 - - - +
333A SER* 1.3 67.0 + - - +
335A GLN* 3.1 18.6 + - - +
336A ASN* 2.9 47.4 + - - +
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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
----------------------------------------------------------
301A ILE* 3.6 30.3 - - - +
329A GLN* 2.8 25.4 + - - +
330A VAL* 3.3 9.8 - - - -
331A THR 3.2 0.2 - - - -
332A VAL* 1.3 76.9 - - - +
334A LEU* 1.3 61.1 + - - +
336A ASN* 3.7 8.8 + - - +
337A LEU* 3.4 25.8 + - - +
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Residues in contact with LEU 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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301A ILE* 4.4 12.8 - - + -
304A ILE* 4.1 17.5 - - + -
305A VAL* 3.9 25.8 - - + -
308A ILE* 4.7 2.2 - - + -
319A ILE* 3.9 26.2 - - + -
330A VAL* 2.8 31.3 + - + +
331A THR 2.8 4.9 + - - +
333A SER* 1.3 70.1 - - - +
335A GLN* 1.3 67.5 + - - +
337A LEU* 3.0 14.2 + - - +
338A GLY 3.3 0.5 + - - -
339A ILE* 3.0 39.9 + - + +
341A ALA* 3.8 19.7 - - + -
367A VAL* 5.6 1.1 - - + -
369A VAL* 4.0 3.8 - - + -
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Residues in contact with GLN 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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331A THR* 2.7 29.7 + - - +
332A VAL* 3.4 20.0 - - - +
334A LEU* 1.3 73.2 - - - +
336A ASN* 1.3 66.5 + - - +
338A GLY* 3.1 14.9 + - - -
339A ILE 3.4 13.4 + - - +
340A HIS* 5.8 0.2 - - - -
341A ALA 3.0 29.0 + - - +
342A GLY* 5.0 1.0 - - - -
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 2.9 38.5 + - - +
333A SER* 3.8 9.4 - - - +
335A GLN* 1.3 77.2 - - - +
337A LEU* 1.3 65.4 + - + +
338A GLY 3.3 1.5 + - - -
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Residues in contact with LEU 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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301A ILE* 3.5 32.1 - - + -
302A GLU* 5.2 9.0 - - + +
305A VAL* 3.9 27.2 - - + +
309A ASN* 5.1 2.8 + - - -
333A SER 3.4 10.0 + - - +
334A LEU 3.0 9.5 + - - +
336A ASN* 1.3 85.7 - - + +
338A GLY* 1.3 54.4 + - - +
339A ILE* 3.4 10.9 + - + +
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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