Contacts of the helix formed by residues 320 - 334 (chain A) in PDB entry 1Z6T
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLY* 4.3 7.5 + - - -
158A CYS* 6.1 0.2 - - - +
284A SER 5.5 2.0 - - - -
317A CYS 3.2 8.4 + - - -
318A LYS* 3.3 4.2 + - - -
319A GLY* 1.3 74.3 - - - +
321A PRO* 1.4 63.5 - - - +
322A LEU* 3.6 8.1 + - - +
323A VAL* 3.2 31.6 + - - +
324A VAL* 2.9 29.6 + - - +
359A TYR* 3.8 17.2 + - - -
364A LEU* 5.4 0.2 - - - +
440A LEU* 5.4 0.3 - - - +
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Residues in contact with PRO 321 (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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129A ARG* 5.1 0.7 - - - +
157A GLY 3.5 22.9 - - - +
158A CYS* 4.0 17.9 - - - +
286A LEU* 4.1 26.0 - - + +
294A ILE* 4.4 4.6 - - + +
319A GLY 3.1 11.4 - - - +
320A SER* 1.4 82.7 - - - +
322A LEU* 1.3 54.9 + - - +
324A VAL* 3.9 9.4 - - + +
325A SER* 2.8 34.0 + - - -
900A ADP 3.6 37.7 - - + +
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Residues in contact with LEU 322 (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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157A GLY* 4.6 3.1 + - - +
320A SER* 3.3 7.9 + - - +
321A PRO* 1.3 77.2 - - - +
323A VAL* 1.3 58.4 + - - +
325A SER* 3.3 1.7 + - - -
326A LEU* 3.0 32.4 + - + +
364A LEU* 3.9 23.6 - - + -
422A SER* 3.9 24.0 - - - +
425A PHE* 4.1 9.6 - - + -
438A HIS* 4.0 34.5 - - + +
440A LEU* 4.7 8.5 - - + -
441A GLN* 4.0 15.7 - - + +
900A ADP 3.3 32.5 + - - +
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Residues in contact with VAL 323 (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 CYS* 3.6 31.6 - - + +
320A SER* 3.2 27.7 + - - +
322A LEU* 1.3 71.9 - - - +
324A VAL* 1.3 67.7 + - - +
325A SER 3.2 0.3 + - - -
326A LEU* 3.2 9.3 + - - +
327A ILE* 3.1 24.5 + - + +
345A LEU* 5.3 2.9 - - + -
359A TYR* 4.7 0.4 - - - +
363A ALA* 3.9 10.1 - - + +
364A LEU* 3.6 38.8 - - + +
367A ALA* 3.8 17.5 - - + -
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Residues in contact with VAL 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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286A LEU* 5.4 1.8 - - + -
291A GLY* 3.4 33.4 - - - +
294A ILE* 3.8 18.9 - - + +
295A LEU* 4.0 7.5 - - + +
314A ILE* 3.8 19.7 - - + -
317A CYS* 3.8 26.0 - - + -
319A GLY* 5.1 3.8 - - - -
320A SER 2.9 26.1 + - - +
321A PRO* 3.9 8.3 - - + +
323A VAL* 1.3 74.9 - - - +
325A SER* 1.3 57.5 + - - +
327A ILE* 3.8 2.0 - - - +
328A GLY* 2.9 26.5 + - - -
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Residues in contact with SER 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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125A VAL 5.2 0.9 + - - -
294A ILE* 3.9 8.3 - - - +
298A PHE* 3.6 24.0 - - - -
321A PRO 2.8 22.3 + - - -
322A LEU 3.5 4.7 - - - -
323A VAL 3.1 0.2 - - - -
324A VAL* 1.3 74.5 - - - +
326A LEU* 1.3 59.5 + - - +
328A GLY 3.4 0.2 + - - -
329A ALA* 3.0 31.4 + - - +
422A SER* 3.7 20.1 + - - -
900A ADP 3.8 23.1 + - - -
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Residues in contact with LEU 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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322A LEU* 3.0 24.8 + - + +
323A VAL* 3.6 6.5 - - - +
325A SER* 1.3 76.6 - - - +
327A ILE* 1.3 59.3 + - - +
329A ALA* 3.6 2.9 + - - +
330A LEU* 3.2 30.0 + - - +
364A LEU* 3.8 23.1 - - + -
367A ALA* 4.1 21.8 - - + +
368A MET* 3.7 25.4 - - + +
371A SER* 4.4 10.4 + - - +
421A LYS 3.7 15.3 - - - +
422A SER* 3.6 23.6 - - - +
423A LEU* 3.7 22.7 - - + -
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Residues in contact with ILE 327 (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 LEU* 4.6 2.0 - - + -
313A ILE* 3.6 30.1 - - + -
317A CYS* 4.2 13.5 - - - -
323A VAL* 3.1 18.2 + - + +
324A VAL* 3.8 3.4 - - - +
326A LEU* 1.3 72.6 - - - +
328A GLY* 1.3 61.7 + - - +
330A LEU* 3.3 22.2 + - + +
331A LEU* 2.9 40.9 + - + +
341A TYR* 5.6 7.4 - - + +
345A LEU* 4.0 24.7 - - + -
367A ALA* 3.8 28.0 - - + -
370A ILE* 4.9 3.6 - - + -
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Residues in contact with GLY 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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295A LEU* 3.7 21.9 - - - +
298A PHE* 3.3 29.2 - - - +
299A VAL* 4.1 1.0 - - - +
324A VAL 2.9 15.7 + - - -
325A SER 3.4 1.3 + - - -
327A ILE* 1.3 77.0 - - - +
329A ALA* 1.3 56.1 + - - +
331A LEU* 3.4 4.6 + - - +
332A ARG* 2.9 23.9 + - - +
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Residues in contact with ALA 329 (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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298A PHE* 3.5 22.5 - - + -
325A SER 3.0 16.9 + - - +
326A LEU 3.7 3.1 - - - +
328A GLY* 1.3 74.2 - - - +
330A LEU* 1.3 58.7 + - - +
332A ARG* 3.4 9.9 + - - +
333A ASP* 3.0 36.3 + - - +
371A SER* 5.9 0.4 - - - +
421A LYS* 3.7 35.7 - - + +
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Residues in contact with LEU 330 (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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326A LEU 3.2 15.2 + - - +
327A ILE* 3.4 25.1 - - + +
329A ALA* 1.3 75.9 - - - +
331A LEU* 1.3 60.0 + - + +
333A ASP* 3.2 4.1 + - - -
334A PHE* 2.8 46.8 + - + +
341A TYR* 4.3 18.1 - - + +
367A ALA 4.7 0.7 - - - +
370A ILE* 3.3 29.4 - - + -
371A SER* 4.0 23.6 - - - +
374A MET* 3.7 34.8 - - + -
421A LYS* 5.4 3.8 - - - +
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Residues in contact with LEU 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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295A LEU* 4.1 12.1 - - + -
299A VAL* 3.8 18.9 - - + +
313A ILE* 3.9 12.6 - - + -
327A ILE* 2.9 30.6 + - + +
328A GLY 3.8 1.3 - - - +
330A LEU* 1.3 74.0 - - + +
332A ARG* 1.3 65.2 + - - +
334A PHE 4.3 4.3 - - - +
335A PRO* 3.2 26.7 - - - +
337A ARG 4.4 0.4 - - - -
338A TRP* 3.5 65.6 + - + +
341A TYR* 3.9 27.4 - - + -
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Residues in contact with ARG 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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124A VAL* 5.5 1.4 - - - +
125A VAL* 5.8 0.4 - - - +
298A PHE* 3.3 46.9 - - - +
299A VAL* 3.8 8.9 - - - +
328A GLY 2.9 11.8 + - - +
329A ALA* 3.5 14.9 + - - +
330A LEU 3.3 0.2 - - - -
331A LEU* 1.3 76.9 - - - +
333A ASP* 1.3 92.4 + - - +
334A PHE 3.6 0.2 + - - -
335A PRO* 3.7 13.6 - - - +
420A ASN* 3.0 39.2 + - - +
421A LYS* 4.2 2.4 - - - +
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Residues in contact with ASP 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 ALA 3.0 21.3 + - - +
330A LEU* 3.7 1.4 + - - +
332A ARG* 1.3 107.7 + - - +
334A PHE* 1.3 87.6 + - + +
335A PRO* 3.7 5.7 - - - +
421A LYS* 2.8 33.9 + - - +
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Residues in contact with PHE 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 LEU* 2.8 24.8 + - + +
331A LEU* 3.5 7.0 - - - +
333A ASP* 1.3 95.3 - - + +
335A PRO* 1.4 65.8 - - - +
336A ASN 3.4 3.6 + - - -
337A ARG* 3.5 38.3 + - + +
341A TYR* 3.4 28.3 - - + +
374A MET* 3.6 42.8 - - + -
421A LYS* 4.3 8.1 - - - -
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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