Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 4XZC
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 THR 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A GLY 4.7 2.2 - - - +
320A ILE* 3.5 23.4 - - + +
321A THR* 2.9 35.4 + - + +
323A VAL* 1.3 78.6 - - - +
325A PHE* 1.3 64.5 + - - +
326A PRO* 3.3 2.2 - - - -
327A THR* 2.8 33.1 + - - +
328A LEU 3.6 1.6 + - - -
354A LEU* 4.3 11.6 - - - +
356A TRP* 3.9 16.2 + - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 4.1 9.6 - - - +
84A CYS* 4.2 7.4 - - + -
89A VAL* 3.6 44.6 - - + -
93A LEU* 5.0 3.4 - - + -
312A TYR* 4.9 3.1 - + - -
315A ALA* 5.4 1.1 - - + -
320A ILE* 3.5 20.0 - - + -
321A THR 2.6 20.4 + - - +
322A PRO 3.9 1.6 - - - +
324A THR* 1.3 72.9 - - - +
326A PRO* 1.4 66.1 - - + +
328A LEU* 2.8 26.4 + - + +
329A SER* 3.0 16.0 + - - -
393A PHE* 3.6 55.2 - + + -
398A VAL* 4.1 23.3 - - + -
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Residues in contact with PRO 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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1A MET 4.0 11.7 - - - +
2A GLU* 4.3 0.7 - - - -
3A ASN* 3.6 26.9 - - + +
322A PRO 3.2 18.2 - - - +
323A VAL 3.4 12.3 - - - +
324A THR 3.5 0.7 - - - -
325A PHE* 1.4 91.7 - - + +
327A THR* 1.3 57.3 + - + +
329A SER* 3.7 2.0 - - - -
330A GLN* 3.0 28.1 + - - +
398A VAL* 3.6 19.7 - - + +
399A SER* 3.1 28.4 + - - +
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Residues in contact with THR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL 5.3 2.0 - - - +
324A THR* 2.8 18.9 + - - +
325A PHE 3.1 0.4 - - - -
326A PRO* 1.3 77.8 - - + +
328A LEU* 1.3 58.8 + - - +
330A GLN* 4.0 5.1 - - - +
331A PHE* 2.9 28.8 + - - +
354A LEU* 3.9 31.9 - - + -
356A TRP* 2.7 33.0 + - - -
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Residues in contact with LEU 328 (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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315A ALA* 4.0 14.4 - - + -
320A ILE* 3.9 32.8 - - + -
324A THR 3.6 0.4 + - - -
325A PHE* 2.8 19.3 + - + +
327A THR* 1.3 77.1 + - - +
329A SER* 1.3 61.6 + - - +
331A PHE* 3.2 2.0 + - + +
332A LEU* 2.9 58.1 + - + +
356A TRP* 3.8 33.0 - - + -
360A ILE* 5.1 6.1 - - + -
386A MET* 5.4 2.2 - - + -
389A MET* 4.0 12.8 - - + -
393A PHE* 3.9 23.8 - - + -
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.0 19.2 + - - -
326A PRO 3.7 8.1 - - - -
328A LEU* 1.3 77.2 - - - +
330A GLN* 1.3 57.6 + - - -
332A LEU 3.8 0.2 - - - -
333A PHE* 2.8 31.8 + - - +
393A PHE* 2.9 30.1 + - - +
396A VAL 3.2 6.1 + - - -
397A PRO* 3.4 1.7 - - - +
398A VAL* 3.2 38.1 + - - +
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO 3.0 19.2 + - - +
327A THR* 4.0 5.8 - - - +
328A LEU 3.3 0.2 - - - -
329A SER* 1.3 71.9 - - - +
331A PHE* 1.3 67.6 + - - +
333A PHE* 3.3 20.8 + - - +
334A GLU* 2.8 56.3 + - + +
397A PRO* 3.5 19.3 - - - +
399A SER* 4.2 9.0 - - - +
400A ASN* 3.5 20.8 + - - +
403A ASP* 5.4 2.8 + - - -
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR 2.9 20.4 + - - +
328A LEU 3.5 4.0 - - - +
330A GLN* 1.3 77.4 - - - +
332A LEU* 1.3 69.3 + - + +
334A GLU* 3.1 9.0 + - + +
335A MET* 2.9 37.2 + - + +
345A MET* 3.8 27.4 - - + -
348A ALA* 3.7 25.6 - - + -
349A LEU* 3.4 39.5 - - + -
352A THR* 6.0 4.9 - - + -
356A TRP* 3.8 20.9 - + + -
386A MET* 4.8 4.3 - - + -
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Residues in contact with LEU 332 (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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328A LEU* 2.9 40.7 + - + +
331A PHE* 1.3 74.6 - - + +
333A PHE* 1.3 64.7 + - - +
335A MET* 3.5 29.8 + - + +
336A GLY 3.4 6.8 + - - -
386A MET* 3.9 26.0 - - + +
389A MET* 3.4 29.4 - - + +
390A GLY* 3.9 11.9 - - - +
393A PHE* 3.7 15.3 - - + -
394A GLY* 3.8 15.0 - - - -
410A HIS* 3.3 22.9 - - - -
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Residues in contact with PHE 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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329A SER 2.8 19.4 + - - +
330A GLN* 3.5 19.7 - - - +
332A LEU* 1.3 73.1 - - - +
334A GLU* 1.3 68.8 + - - +
336A GLY 3.2 2.1 + - - -
337A GLN* 3.3 31.5 - - - +
394A GLY* 3.4 23.2 - - - +
395A VAL 3.5 20.9 - - - -
397A PRO* 3.7 30.5 - - + -
403A ASP* 3.4 32.3 - - + -
404A ALA* 4.2 2.5 - - - -
406A LEU* 4.4 4.3 - - + -
407A GLY 3.6 20.9 - - - -
408A SER* 2.8 24.1 + - - -
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Residues in contact with GLU 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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330A GLN* 2.8 52.6 + - + +
331A PHE* 3.4 8.7 - - + +
333A PHE* 1.3 78.3 - - - +
335A MET* 1.3 64.3 + - - +
337A GLN* 2.9 40.3 + - - +
340A ARG* 3.1 31.6 + - - +
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Residues in contact with MET 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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68A VAL* 5.7 0.2 - - - +
331A PHE* 2.9 24.3 + - + +
332A LEU* 3.6 25.4 - - + +
333A PHE 3.2 0.4 - - - -
334A GLU* 1.3 76.3 - - - +
336A GLY* 1.3 56.2 + - - +
338A GLY 3.2 19.6 - - - +
340A ARG* 3.7 33.6 + - - +
341A GLY* 4.4 5.9 + - - +
345A MET* 4.0 26.7 - - - +
386A MET* 3.6 28.9 - - + +
387A SER* 4.6 3.1 - - - -
390A GLY* 4.3 0.2 - - - -
410A HIS* 4.0 25.4 - - + +
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Residues in contact with GLY 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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68A VAL* 3.5 13.6 - - - +
72A LYS* 5.1 0.5 - - - +
332A LEU 3.4 4.2 + - - -
333A PHE 3.2 3.8 + - - -
334A GLU 3.1 1.4 - - - -
335A MET* 1.3 78.1 - - - +
337A GLN* 1.3 55.2 + - - +
338A GLY 3.2 8.9 + - - -
408A SER* 3.3 20.2 - - - -
409A GLY* 2.8 31.3 + - - +
410A HIS* 3.9 10.5 - - - -
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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