Contacts of the helix formed by residues 312 - 329 (chain A) in PDB entry 4LZ6
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 TYR 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN 3.9 8.7 - - - -
307A TYR* 4.2 26.7 - + - -
308A GLY 4.0 19.5 + - - -
309A ALA* 4.3 8.1 - - - -
310A LYS 2.7 32.2 + - - -
311A GLN* 1.3 70.1 - - - +
313A SER* 1.3 62.4 + - - +
315A LEU* 3.1 23.5 + - + +
316A ARG* 3.5 19.5 + - - +
446A PHE* 4.1 28.0 - + + -
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLN* 4.2 8.8 - - - +
312A TYR* 1.3 79.7 - - - +
314A ARG* 1.3 72.1 + - - +
315A LEU 3.7 0.5 + - - -
316A ARG* 3.6 29.4 + - - +
317A GLU* 4.1 13.0 + - - +
447A LEU* 5.9 1.0 - - - +
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Residues in contact with ARG 314 (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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13A GLU* 2.6 55.3 + - + +
15A ILE* 3.1 35.2 - - + +
306A ASN* 4.5 1.6 + - - -
311A GLN* 2.9 17.4 + - + +
313A SER* 1.3 88.4 + - - +
315A LEU* 1.3 57.5 + - - +
317A GLU* 3.9 19.6 + - - +
318A THR* 3.5 1.7 + - - -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 4.0 30.1 - - + +
306A ASN* 4.2 15.7 - - + -
307A TYR* 4.2 29.2 - - + +
311A GLN 3.4 2.0 + - - +
312A TYR* 3.1 23.8 + - + +
314A ARG* 1.3 77.2 - - - +
316A ARG* 1.3 88.5 + - + +
317A GLU 2.8 2.0 - - - -
318A THR* 2.7 11.5 + - - +
319A VAL* 2.7 29.2 + - + +
385A LEU* 4.7 8.1 - - + -
443A ASN 4.9 2.5 - - - +
444A VAL* 3.6 24.0 - - + +
446A PHE* 4.7 6.3 - - + -
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A TYR* 3.5 9.0 - - - +
313A SER* 3.6 34.4 + - - +
315A LEU* 1.3 81.7 - - + +
317A GLU* 1.3 54.3 + - - +
319A VAL* 4.0 3.8 - - - +
320A MET* 2.5 38.1 + - - +
444A VAL 4.0 9.9 - - - +
445A PHE* 4.5 3.4 - - + -
446A PHE* 2.9 71.7 + - + -
447A LEU* 3.9 39.8 - - + +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 29.3 - - + +
16A PRO* 5.6 4.0 - - + -
313A SER 4.1 5.4 + - - +
314A ARG* 3.6 35.7 + - - +
316A ARG* 1.3 75.0 - - - +
318A THR* 1.3 67.7 + - - +
320A MET* 4.3 8.4 - - + +
321A LEU* 3.1 22.3 + - + +
447A LEU* 4.4 9.0 - - + +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.4 17.4 - - + +
19A LEU* 3.8 29.2 - - + -
299A MET* 4.1 6.5 - - + -
302A ILE* 3.3 37.2 - - + +
303A VAL* 3.9 14.1 - - + +
314A ARG 3.5 4.7 + - - -
315A LEU* 2.7 15.8 + - - -
317A GLU* 1.3 69.8 - - - +
319A VAL* 1.3 59.8 + - - +
321A LEU* 2.5 32.8 + - - -
322A GLY* 2.7 8.5 + - - -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 5.2 0.9 - - - -
303A VAL* 4.0 22.4 - - + -
315A LEU* 2.7 32.4 + - + +
316A ARG* 4.0 5.6 - - - +
318A THR* 1.3 73.2 - - - +
320A MET* 1.3 66.4 + - - +
322A GLY* 3.8 2.6 - - - +
323A PHE* 3.1 30.2 + - + -
381A LEU* 3.6 23.3 - - + -
444A VAL* 3.5 47.6 - - + +
445A PHE* 4.0 13.7 - - + +
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Residues in contact with MET 320 (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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316A ARG 2.5 18.7 + - - +
317A GLU* 4.3 8.7 - - + +
318A THR 2.6 1.2 + - - -
319A VAL* 1.3 72.8 - - - +
321A LEU* 1.3 78.8 + - + +
322A GLY 3.0 0.3 + - - -
323A PHE* 3.1 6.1 + - + +
324A LYS* 2.8 36.8 + - + +
445A PHE* 3.0 39.9 - - + -
447A LEU* 4.2 15.7 - - + -
448A LYS* 5.3 6.1 - - - -
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Residues in contact with LEU 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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15A ILE* 6.5 0.4 - - + -
16A PRO* 4.4 23.1 - - + -
19A LEU* 3.2 33.9 - - + -
20A ARG* 4.0 23.3 - - - +
317A GLU* 3.1 19.0 + - + +
318A THR* 2.5 9.6 + - - +
320A MET* 1.3 83.2 - - + +
322A GLY* 1.3 53.8 + - - +
324A LYS* 2.9 16.8 - - + +
325A VAL* 2.6 38.8 + - + +
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Residues in contact with GLY 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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19A LEU* 4.5 0.6 - - - +
295A ILE* 4.4 1.2 - - - +
299A MET* 2.7 40.0 - - - +
318A THR 2.7 16.3 + - - -
319A VAL 3.8 1.1 - - - -
321A LEU* 1.3 74.4 - - - +
323A PHE* 1.3 65.2 + - - +
325A VAL* 3.3 6.3 - - - +
326A ALA* 3.2 18.9 + - - +
377A VAL* 4.2 5.0 - - - +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.1 18.9 + - + -
320A MET* 3.1 10.7 + - - +
322A GLY* 1.3 73.9 - - - +
324A LYS* 1.3 67.8 + - - +
326A ALA* 3.0 2.0 + - - +
327A THR* 2.8 29.3 + - - +
374A ALA* 4.5 21.3 - - + +
377A VAL* 3.1 41.3 - - + -
378A ALA* 4.0 8.1 - - - -
381A LEU* 3.7 20.4 - - + -
438A LEU* 3.4 36.1 - - + -
444A VAL* 6.2 1.3 - - + -
445A PHE* 6.0 11.0 - + + -
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Residues in contact with LYS 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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320A MET* 2.8 29.0 + - + +
321A LEU* 2.9 27.1 + - + +
323A PHE* 1.3 72.2 - - - +
325A VAL* 1.3 67.2 + - - +
327A THR* 3.1 12.3 + - - -
328A ILE* 3.3 9.0 + - - +
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.7 5.4 - - + -
20A ARG* 4.6 21.5 - - - +
295A ILE* 3.8 27.6 - - + -
321A LEU* 2.6 30.4 + - + +
322A GLY* 3.3 17.3 - - - +
324A LYS* 1.3 72.7 - - - +
326A ALA* 1.3 69.0 + - - +
328A ILE* 2.5 27.8 + - + +
329A PHE* 3.2 38.7 + - + -
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Residues in contact with ALA 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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292A MET* 3.3 21.0 - - + +
295A ILE* 4.6 5.8 - - + +
322A GLY 3.2 6.4 + - - +
323A PHE 3.0 10.6 + - - +
325A VAL* 1.3 77.9 - - - +
327A THR* 1.3 53.5 + - - +
329A PHE* 2.8 7.4 + - - +
330A SER* 2.7 32.2 + - - -
373A GLY* 3.7 12.6 - - - +
377A VAL* 3.5 30.1 - - + -
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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
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323A PHE* 2.8 19.2 + - - +
324A LYS* 3.5 10.1 - - - -
325A VAL 2.7 4.0 + - - -
326A ALA* 1.3 71.0 - - - +
328A ILE* 1.3 55.1 + - - +
330A SER* 2.7 35.0 + - - -
331A ILE* 3.3 19.4 + - + +
370A PHE 5.2 3.8 + - - +
373A GLY* 4.8 0.6 - - - -
374A ALA* 4.8 13.0 + - - +
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Residues in contact with ILE 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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324A LYS 3.3 4.0 + - - +
325A VAL* 2.5 27.3 + - + +
327A THR* 1.3 76.3 - - - +
329A PHE* 1.3 74.5 + - + +
330A SER 3.1 0.2 - - - -
331A ILE* 3.0 35.8 - - + +
332A GLY* 3.1 7.3 + - - -
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Residues in contact with PHE 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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20A ARG* 6.1 1.6 - - - -
27A MET* 5.3 2.2 - - + -
291A PRO* 4.4 15.9 - - + -
292A MET* 3.2 26.9 - - - +
295A ILE* 4.2 20.4 - - + -
325A VAL* 3.2 34.8 + - + -
326A ALA 2.8 8.3 + - - +
328A ILE* 1.3 84.8 - - + +
330A SER* 1.3 62.8 + - - +
332A GLY* 3.5 8.3 - - - +
333A ILE* 3.4 21.6 + - + +
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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
------------------------------------------------------------
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