Contacts of the helix formed by residues 316 - 332 (chain A) in PDB entry 4LVA
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 ASN 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLY* 1.3 69.0 - - - -
317A PRO* 1.3 74.5 - - - +
318A LEU* 3.1 10.6 + - - +
319A ASP* 2.9 51.0 + - + +
320A THR* 2.8 26.7 + - - -
608A EDO 4.9 1.3 - - - -
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Residues in contact with PRO 317 (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 GLY 3.1 5.8 - - - +
316A ASN* 1.3 90.6 - - - +
318A LEU* 1.3 62.2 + - - +
320A THR* 4.8 0.7 - - - -
321A VAL* 3.1 29.8 + - - +
352A GLN* 3.5 13.1 + - - +
354A ASP* 3.9 20.2 - - - +
355A GLY 4.4 9.4 - - - +
360A THR* 5.2 7.4 - - + -
364A ILE* 3.9 22.9 - - + -
608A EDO 3.6 26.2 - - - -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 3.1 8.4 + - - +
317A PRO* 1.3 76.9 - - - +
319A ASP* 1.3 73.6 + - - +
321A VAL* 3.2 3.9 + - + +
322A LEU* 3.0 46.5 + - + +
363A GLU* 3.7 20.4 - - + +
364A ILE* 3.6 44.6 - - + +
367A GLY* 3.8 15.5 - - - -
368A MET* 4.9 0.9 - - + -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 5.1 0.7 - - - -
316A ASN* 2.9 36.1 + - + +
318A LEU* 1.3 84.7 - - - +
320A THR* 1.3 58.4 + - - +
322A LEU* 3.5 9.8 + - - +
323A LYS* 3.0 29.5 + - - +
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Residues in contact with THR 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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283A ILE* 4.8 4.3 - - + -
284A TYR* 3.3 29.3 + - + +
312A PRO* 3.8 25.4 - - + -
314A SER 3.2 25.1 + - - +
315A GLY* 3.6 7.1 - - - -
316A ASN 2.8 19.3 + - - -
317A PRO* 4.1 4.0 - - - -
319A ASP* 1.3 75.4 - - - +
321A VAL* 1.3 59.1 + - - +
323A LYS* 3.3 1.3 + - - +
324A VAL* 2.9 38.5 + - + +
352A GLN* 4.8 2.9 - - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PRO* 4.9 6.1 - - + -
317A PRO 3.1 19.3 + - - +
318A LEU 3.2 3.8 + - - +
320A THR* 1.3 76.0 - - - +
322A LEU* 1.3 63.4 + - + +
324A VAL* 3.4 5.8 + - - +
325A LEU* 2.9 42.9 + - + +
350A VAL* 5.3 4.9 - - + -
352A GLN* 3.5 26.0 - - + +
364A ILE* 4.4 8.5 - - + -
368A MET* 4.0 13.2 - - + -
378A ILE* 3.6 33.7 - - + -
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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
----------------------------------------------------------
318A LEU* 3.0 47.1 + - + +
319A ASP* 3.9 8.5 - - - +
321A VAL* 1.3 75.6 - - - +
323A LYS* 1.3 58.7 + - - +
325A LEU* 3.4 4.4 + - + +
326A GLU* 2.9 30.0 + - - +
367A GLY* 3.9 18.4 - - - +
368A MET* 4.1 18.8 - - + -
371A LYS* 4.0 41.3 - - + +
373A TRP* 4.5 10.8 + - + +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 3.5 55.9 - - + +
319A ASP 3.0 18.3 + - - +
320A THR 3.8 3.1 - - - +
322A LEU* 1.3 74.1 - - - +
324A VAL* 1.3 59.5 + - - +
326A GLU* 3.3 16.5 + - - +
327A ILE* 2.9 37.3 + - + +
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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
----------------------------------------------------------
283A ILE* 4.0 27.1 - - + -
284A TYR* 4.4 5.2 - - + -
287A CYS* 4.1 15.5 - - - -
310A ILE* 4.6 4.9 - - + -
312A PRO* 4.3 10.3 - - + -
320A THR* 2.9 28.0 + - + +
321A VAL* 3.7 6.1 - - - +
323A LYS* 1.3 75.9 - - - +
325A LEU* 1.3 58.0 + - - +
327A ILE* 3.3 8.3 + - - +
328A LEU* 2.9 49.6 + - + +
350A VAL* 4.2 19.5 - - + -
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Residues in contact with LEU 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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321A VAL* 2.9 40.7 + - + +
322A LEU* 3.7 5.8 - - - +
324A VAL* 1.3 74.4 - - + +
326A GLU* 1.3 58.5 + - - +
328A LEU* 3.4 4.0 + - + +
329A GLY 2.8 25.8 + - - -
344A LEU* 4.1 26.5 - - + -
350A VAL* 4.1 16.6 - - + -
368A MET* 3.8 19.7 - - + -
373A TRP* 3.3 56.8 - - + +
377A ASN* 4.3 8.5 - - + -
378A ILE* 5.7 0.4 - - + -
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Residues in contact with GLU 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 2.9 17.0 + - - +
323A LYS* 3.6 19.6 - - - +
324A VAL 3.3 0.2 - - - -
325A LEU* 1.3 76.6 - - - +
327A ILE* 1.3 64.5 + - + +
329A GLY* 3.3 7.6 + - - -
330A LYS* 3.4 38.4 + - + +
373A TRP* 4.1 10.0 - - + +
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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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284A TYR* 3.7 47.3 - - + +
287A CYS* 3.7 13.5 - - + +
288A GLU* 3.5 53.1 - - + +
323A LYS* 2.9 30.6 + - + +
324A VAL* 3.6 4.5 - - - +
326A GLU* 1.3 78.4 - - + +
328A LEU* 1.3 64.1 + - - +
330A LYS* 3.2 14.4 + - - +
331A LYS* 3.3 14.6 + - + +
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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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287A CYS* 4.1 24.2 - - + +
291A TRP* 5.1 0.7 - - + -
310A ILE* 3.7 33.9 - - + -
324A VAL* 2.9 36.7 + - + +
325A LEU* 4.0 4.0 - - - +
327A ILE* 1.3 75.1 - - - +
329A GLY* 1.3 57.7 + - - +
331A LYS* 3.1 1.4 + - + -
332A PHE* 2.9 56.6 + - + +
344A LEU* 4.1 17.7 - - + -
348A LEU* 4.1 15.0 - - + -
350A VAL* 4.1 16.6 - - + -
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Residues in contact with GLY 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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325A LEU 2.8 17.5 + - - -
326A GLU 3.9 1.6 - - - -
327A ILE 3.2 0.6 - - - -
328A LEU* 1.3 76.4 - - - +
330A LYS* 1.3 61.9 + - - +
332A PHE 3.2 14.9 - - - +
334A VAL* 3.6 27.7 - - - +
344A LEU* 4.7 0.4 - - - -
373A TRP* 4.2 8.5 - - - -
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Residues in contact with LYS 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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288A GLU* 6.1 0.2 - - - +
326A GLU* 3.4 32.2 + - + +
327A ILE* 3.2 9.3 + - - +
328A LEU 3.1 0.4 - - - -
329A GLY* 1.3 82.0 - - - +
331A LYS* 1.3 67.2 + - + +
332A PHE 3.5 0.7 - - - -
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Residues in contact with LYS 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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287A CYS 4.9 0.7 - - - +
288A GLU* 3.3 46.1 - - + +
292A GLY* 3.7 16.2 - - - +
293A GLU* 2.8 31.5 + - - +
296A ARG* 2.8 34.5 + - - -
327A ILE* 3.4 16.2 - - + +
328A LEU* 3.1 2.2 + - - -
330A LYS* 1.3 88.4 - - + +
332A PHE* 1.3 70.5 + - + +
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Residues in contact with PHE 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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291A TRP* 3.6 21.5 - - + -
292A GLY* 4.1 16.2 - - - -
296A ARG* 3.6 23.3 - - + -
299A ILE* 3.8 31.0 - - + -
300A VAL* 3.9 11.2 - - + -
328A LEU* 2.9 32.5 + - + +
329A GLY 3.2 19.2 - - - +
330A LYS 4.6 0.7 - - - -
331A LYS* 1.3 85.3 + - + +
333A PRO* 1.3 66.8 - - + +
334A VAL* 3.2 7.3 + - - +
344A LEU* 5.2 0.9 - - + -
345A PRO* 3.9 15.3 - - + -
347A TYR* 4.0 17.7 - + - -
348A LEU* 3.6 20.2 - - + -
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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