Contacts of the helix formed by residues 320 - 334 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B MET* 6.0 6.1 - - - -
157B GLY* 4.3 6.6 + - - -
284B SER 5.5 1.8 - - - -
317B CYS 3.2 7.5 + - - -
318B LYS* 3.2 6.2 + - - -
319B GLY* 1.3 73.9 - - - +
321B PRO* 1.3 62.9 - - - +
322B LEU* 3.5 8.8 + - - +
323B VAL* 3.3 33.0 + - - +
324B VAL* 2.9 29.6 + - - +
359B TYR* 4.2 14.2 + - - -
364B LEU* 5.4 0.3 - - - +
440B LEU* 5.7 0.5 - - - +
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Residues in contact with PRO 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.1 0.2 - - - +
157B GLY 3.3 24.7 - - - +
158B CYS* 3.9 19.7 - - - +
284B SER 5.6 0.2 - - - +
286B LEU* 4.2 25.4 - - + +
294B ILE* 4.5 2.0 - - + +
319B GLY 3.1 10.7 - - - +
320B SER* 1.3 83.2 - - - +
322B LEU* 1.3 51.3 + - - +
324B VAL* 3.9 8.8 - - + +
325B SER* 2.7 36.4 + - - -
901B ADP 3.5 39.2 + - + +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLY* 4.9 3.8 - - - +
320B SER* 3.2 9.0 + - - +
321B PRO* 1.3 74.0 - - - +
323B VAL* 1.3 60.3 + - - +
325B SER* 3.3 2.9 + - - -
326B LEU* 2.9 35.3 + - + +
364B LEU* 3.9 23.1 - - + -
422B SER* 4.0 11.2 - - - +
425B PHE* 4.1 10.3 - - + -
438B HIS* 4.0 36.1 - - + +
440B LEU* 4.7 10.3 - - + -
441B GLN* 3.8 25.8 - - + +
901B ADP 3.2 34.2 + - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B CYS* 3.6 30.3 - - + +
320B SER* 3.1 28.6 + - - +
322B LEU* 1.3 71.8 - - - +
324B VAL* 1.3 67.8 + - - +
326B LEU* 3.1 9.3 + - - +
327B ILE* 3.1 24.6 + - + +
345B LEU* 5.2 1.8 - - + -
359B TYR* 5.0 1.1 - - - +
363B ALA* 3.9 12.3 - - + +
364B LEU* 3.7 35.0 - - + +
367B ALA* 3.8 19.5 - - + -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 5.3 1.8 - - + -
291B GLY* 3.4 32.5 - - - +
294B ILE* 3.7 18.7 - - + +
295B LEU* 3.8 8.0 - - + +
314B ILE* 3.8 20.0 - - + -
317B CYS* 3.8 24.7 - - + -
319B GLY* 5.0 4.3 - - - -
320B SER 2.9 25.7 + - - +
321B PRO* 4.0 7.2 - - + +
323B VAL* 1.3 75.7 - - - +
325B SER* 1.3 57.7 + - - +
327B ILE* 3.4 2.8 + - - +
328B GLY* 2.8 27.5 + - - -
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 5.9 0.2 - - - -
125B VAL 5.2 1.0 + - - -
294B ILE* 4.1 4.9 - - - +
298B PHE* 3.6 23.9 - - - -
321B PRO 2.7 22.6 + - - -
322B LEU 3.5 5.4 - - - -
323B VAL 3.1 0.2 - - - -
324B VAL* 1.3 74.3 - - - +
326B LEU* 1.3 64.7 + - - +
329B ALA* 3.0 26.2 + - - +
422B SER* 3.6 20.5 + - - -
901B ADP 3.7 26.0 + - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 2.9 24.8 + - + +
323B VAL* 3.1 6.0 + - - +
325B SER* 1.3 77.5 - - - +
327B ILE* 1.3 61.9 + - - +
329B ALA* 3.6 3.5 + - - +
330B LEU* 3.2 26.7 + - - +
364B LEU* 3.7 27.8 - - + -
367B ALA* 4.0 23.3 - - + +
368B MET* 3.8 18.4 - - + +
371B SER* 4.5 7.6 + - - +
421B LYS 3.7 15.7 - - - +
422B SER* 3.4 26.0 - - - +
423B LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.8 1.3 - - + -
313B ILE* 3.8 28.7 - - + -
317B CYS* 4.2 9.6 - - - -
323B VAL 3.1 15.3 + - - +
324B VAL* 3.8 5.2 - - - +
326B LEU* 1.3 74.0 - - - +
328B GLY* 1.3 59.7 + - - +
330B LEU* 3.1 21.8 + - + +
331B LEU* 2.9 43.0 + - + +
341B TYR* 5.2 8.5 - - + -
345B LEU* 4.0 28.9 - - + -
367B ALA* 3.9 24.0 - - + -
370B ILE* 4.8 5.2 - - + -
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Residues in contact with GLY 328 (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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295B LEU* 3.7 18.3 - - - +
298B PHE* 3.3 32.3 - - - +
324B VAL 2.8 20.9 + - - -
327B ILE* 1.3 73.2 - - - +
329B ALA* 1.3 55.2 + - - +
331B LEU* 3.3 6.3 + - - +
332B ARG* 2.9 24.1 + - - +
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Residues in contact with ALA 329 (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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298B PHE* 3.6 18.0 - - + -
325B SER 3.0 17.3 + - - +
326B LEU 3.7 5.2 - - - +
328B GLY* 1.3 72.0 - - - +
330B LEU* 1.3 65.6 + - - +
332B ARG* 3.3 18.6 + - - +
333B ASP* 3.0 32.5 + - - +
371B SER* 6.1 0.2 - - - +
421B LYS* 3.8 27.4 - - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU 3.2 15.2 + - - +
327B ILE* 3.1 25.1 + - + +
329B ALA* 1.3 77.9 - - - +
331B LEU* 1.3 58.3 + - - +
333B ASP* 3.1 2.6 + - - -
334B PHE* 2.8 42.9 + - + +
341B TYR* 4.0 21.1 - - + +
367B ALA 4.7 0.4 - - - +
370B ILE* 3.5 29.6 - - + -
371B SER* 3.9 28.3 - - - +
374B MET* 3.8 32.1 - - + -
421B LYS* 4.9 4.3 - - - +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.4 11.4 - - + -
299B VAL* 3.7 16.8 - - + +
313B ILE* 4.2 5.2 - - + -
327B ILE* 2.9 35.4 + - + +
328B GLY* 3.7 4.7 - - - +
330B LEU* 1.3 76.9 - - - +
332B ARG* 1.3 61.9 + - - +
334B PHE 4.3 5.6 - - - +
335B PRO* 3.1 27.5 - - - +
337B ARG 4.3 1.1 - - - +
338B TRP* 3.4 74.9 + - + +
341B TYR* 4.1 15.9 - - + -
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Residues in contact with ARG 332 (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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124B VAL* 5.5 2.4 - - - +
125B VAL* 5.8 0.4 - - - +
298B PHE* 3.2 47.5 - - - +
299B VAL* 4.0 6.9 - - - +
328B GLY 2.9 16.0 + - - +
329B ALA* 3.5 12.5 + - - +
330B LEU 3.2 0.2 - - - -
331B LEU* 1.3 78.8 - - - +
333B ASP* 1.3 90.4 + - - +
335B PRO* 3.4 15.7 - - - +
420B ASN* 3.0 40.0 + - - +
421B LYS* 4.2 1.8 - - - +
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Residues in contact with ASP 333 (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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329B ALA 3.0 22.6 + - - +
330B LEU* 3.1 1.1 + - - -
332B ARG* 1.3 108.1 + - - +
334B PHE* 1.3 91.0 + - + +
335B PRO* 3.5 5.8 - - - +
421B LYS* 3.2 31.7 + - - +
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Residues in contact with PHE 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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330B LEU* 2.8 23.9 + - + +
331B LEU* 3.6 6.5 - - - +
333B ASP* 1.3 98.0 - - + +
335B PRO* 1.3 66.3 - - - +
336B ASN 3.5 2.2 - - - -
337B ARG* 3.3 42.5 + - - +
341B TYR* 3.2 25.4 - - - +
374B MET* 3.6 41.1 - - + -
421B LYS* 3.9 14.6 - - - -
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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