Contacts of the helix formed by residues 320 - 334 (chain A) in PDB entry 1LVK
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 ASP 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ARG* 2.8 44.5 + - - -
279A HIS* 5.2 1.0 - - - +
282A TYR* 3.6 29.8 - - + +
283A GLN* 3.8 12.9 - - - +
286A ALA* 4.1 4.0 - - + -
313A VAL 4.2 3.5 - - - +
314A ASP* 4.4 7.3 - - - +
315A ILE 4.8 0.9 + - - -
318A VAL* 3.8 17.8 + - - +
319A SER* 1.3 70.9 - - - +
321A GLU* 1.3 60.4 + - - +
323A GLU* 3.0 7.5 + - - +
324A PHE* 2.7 36.0 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ALA* 2.9 37.0 - - - +
287A GLY* 4.0 15.9 - - - +
318A VAL 5.0 0.2 - - - +
319A SER* 2.7 33.8 + - - +
320A ASP* 1.3 77.0 + - - +
322A ASP* 1.3 62.7 + - - +
324A PHE 3.4 2.4 + - - -
325A LYS* 2.7 34.6 - - + -
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Residues in contact with ASP 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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319A SER* 2.7 38.0 + - - +
321A GLU* 1.3 79.5 - - - +
323A GLU* 1.3 64.4 + - + +
325A LYS* 3.3 18.2 - - - +
326A ILE* 3.3 18.5 - - + +
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Residues in contact with GLU 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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283A GLN* 3.5 23.3 - - + +
318A VAL* 4.1 19.5 - - + +
319A SER 2.7 16.4 + - - +
320A ASP* 3.4 9.4 - - - +
322A ASP* 1.3 75.8 - - - +
324A PHE* 1.3 60.3 + - - +
325A LYS 3.1 1.6 - - - -
326A ILE* 3.0 32.0 + - - +
327A THR* 2.8 31.5 + - - -
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Residues in contact with PHE 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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280A ILE* 5.1 3.4 - - + -
283A GLN* 3.1 41.0 - - + +
284A LEU* 3.6 25.1 - - + -
287A GLY* 3.2 30.3 - - - -
288A ALA* 3.6 7.2 - - - -
292A GLU* 5.1 0.2 - - - -
320A ASP 2.7 15.5 + - - +
321A GLU 3.4 7.8 + - - +
323A GLU* 1.3 73.4 - - - +
325A LYS* 1.3 66.0 + - - +
327A THR* 3.2 3.6 + - + -
328A ARG* 2.8 70.5 + - + +
331A MET* 5.3 1.1 - - + -
345A PHE* 3.7 34.1 - + - -
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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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287A GLY* 3.0 31.5 + - - -
321A GLU* 2.7 30.0 - - + +
322A ASP* 3.3 16.5 + - - +
323A GLU 3.1 0.2 - - - -
324A PHE* 1.3 87.2 - - - +
326A ILE* 1.3 59.0 + - + +
328A ARG* 3.2 16.7 + - - +
329A GLN* 2.7 46.6 + - - +
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Residues in contact with ILE 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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217A GLN* 4.9 4.6 - - - +
220A PRO* 4.8 15.7 - - + -
322A ASP* 3.3 14.1 - - + +
323A GLU* 3.2 37.0 - - - +
325A LYS* 1.3 77.6 - - + +
327A THR* 1.3 58.2 + - - +
329A GLN* 3.0 13.8 - - + +
330A ALA* 2.9 29.7 + - - +
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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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220A PRO* 4.2 9.2 + - - +
221A ILE* 4.7 4.6 - - - +
224A ALA* 3.7 22.0 - - + +
225A PHE* 4.7 10.1 - - + -
280A ILE* 4.9 4.5 - - + -
283A GLN* 2.9 32.6 + - - +
323A GLU* 2.8 10.1 + - - +
324A PHE* 3.6 8.3 - - + -
325A LYS 3.1 0.2 - - - -
326A ILE* 1.3 78.8 - - - +
328A ARG* 1.3 61.1 + - - +
330A ALA* 3.3 8.0 + - - +
331A MET* 3.0 42.4 + - + +
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Residues in contact with ARG 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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287A GLY 3.3 24.4 + - - -
289A THR* 4.6 5.7 - - - +
292A GLU* 2.8 36.5 + - - -
324A PHE* 2.8 41.3 + - + +
325A LYS* 3.4 20.5 - - - +
327A THR* 1.3 69.5 - - - +
329A GLN* 1.3 66.6 + - - +
331A MET* 3.2 10.5 + - + +
332A ASP* 3.0 32.4 + - - +
338A GLN* 5.3 3.1 - - - -
341A GLN* 4.0 9.5 - - - +
342A MET* 4.6 10.5 - - - +
345A PHE* 3.8 28.7 - - + -
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLN* 4.9 3.8 - - - +
325A LYS* 2.7 30.4 + - - +
326A ILE* 3.0 12.7 - - + +
328A ARG* 1.3 72.6 - - - +
330A ALA* 1.3 62.3 + - - +
332A ASP* 3.0 23.5 - - - +
333A ILE* 2.8 30.7 - - + +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLN* 3.4 44.2 + - - +
220A PRO* 4.1 9.6 - - + -
221A ILE* 3.7 10.8 - - + -
326A ILE 2.9 14.8 + - - +
327A THR 3.6 7.9 - - - +
329A GLN* 1.3 73.1 - - - +
331A MET* 1.3 59.9 + - - +
333A ILE* 3.1 4.4 + - - +
334A VAL* 2.8 33.4 + - - +
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Residues in contact with MET 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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221A ILE* 3.9 15.9 - - + +
225A PHE* 5.2 6.1 - - + -
327A THR* 3.0 37.7 + - + +
328A ARG* 3.2 19.5 + - + +
330A ALA* 1.3 75.1 - - - +
332A ASP* 1.3 55.0 + - - +
335A GLY 2.8 8.3 + - - -
336A PHE* 2.5 51.5 + - + +
341A GLN* 3.7 27.8 - - - +
344A ILE* 4.4 20.6 - - - -
345A PHE* 3.0 39.0 - - + -
433A LEU* 6.0 0.9 - - - -
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Residues in contact with ASP 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 ARG* 3.0 22.8 + - - +
329A GLN* 3.0 15.0 - - - +
331A MET* 1.3 77.3 - - - +
333A ILE* 1.3 66.1 + - + +
335A GLY* 3.2 13.7 + - - -
336A PHE 4.4 2.4 - - - +
338A GLN* 3.6 13.3 + - - -
341A GLN* 3.0 23.7 + - - +
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Residues in contact with ILE 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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213A GLN* 4.0 18.8 - - + +
214A GLN* 3.7 33.0 + - + +
217A GLN* 3.8 29.6 - - + +
329A GLN* 2.8 49.7 + - + +
330A ALA* 3.6 7.4 - - - +
332A ASP* 1.3 80.5 - - + +
334A VAL* 1.3 72.4 + - - +
335A GLY* 3.2 0.5 + - - -
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Residues in contact with VAL 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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214A GLN* 3.3 44.9 + - + +
217A GLN* 4.1 10.1 - - + -
218A ALA* 4.3 3.6 - - + +
221A ILE* 3.8 18.6 - - + -
330A ALA 2.8 22.8 + - - +
331A MET 4.2 2.0 - - - +
333A ILE* 1.3 75.5 - - - +
335A GLY* 1.3 59.6 + - - +
336A PHE* 4.2 15.9 - - + -
437A ILE* 4.3 18.8 - - + -
440A VAL* 3.8 32.2 - - + +
441A LEU* 5.4 1.3 - - + -
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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