Contacts of the helix formed by residues 315 - 327 (chain L) in PDB entry 4XLN
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 315 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307L ALA* 3.3 9.9 - - - +
313L GLY 3.6 7.4 + - - +
314L TRP* 1.3 74.8 - - - +
316L ALA* 1.3 64.6 + - - +
317L LYS* 3.4 10.0 + - - +
318L ARG* 2.8 38.9 + - - +
319L VAL* 3.2 22.0 + - - +
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Residues in contact with ALA 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808I ARG* 5.4 9.2 - - - +
303L TYR* 3.4 36.2 + - + +
304L GLU* 4.4 6.0 - - + +
307L ALA* 4.1 0.2 - - - +
315L ASP* 1.3 75.0 - - - +
317L LYS* 1.3 58.8 + - - +
319L VAL* 3.1 3.7 - - - +
320L GLU* 2.9 32.9 + - - +
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Residues in contact with LYS 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714I ASP* 4.3 21.7 + - - -
808I ARG* 4.9 12.7 - - - +
820I ARG* 5.5 4.9 - - - +
315L ASP* 3.3 10.6 + - - +
316L ALA* 1.3 79.7 - - - +
318L ARG* 1.3 58.5 + - - +
320L GLU* 3.7 21.6 + - - +
321L GLU* 2.9 36.9 + - + +
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Residues in contact with ARG 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282L THR* 4.6 11.5 - - - +
312L PRO 4.8 1.4 + - - -
313L GLY* 4.0 18.9 + - - -
314L TRP* 3.3 61.3 - - + +
315L ASP* 2.8 23.1 + - - +
317L LYS* 1.3 75.0 - - - +
319L VAL* 1.3 60.8 + - - +
321L GLU* 3.0 8.5 + - + +
322L THR* 2.9 37.6 + - + +
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Residues in contact with VAL 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286L LEU* 3.7 26.1 - - + +
303L TYR* 3.6 30.5 - - + +
306L ILE* 3.7 22.4 - - + -
307L ALA* 4.0 3.6 - - + -
314L TRP* 4.0 14.3 - - + -
315L ASP 3.2 13.9 + - - +
316L ALA* 3.1 15.7 - - - +
318L ARG* 1.3 78.0 - - - +
320L GLU* 1.3 55.8 + - - +
322L THR* 3.1 8.1 + - - -
323L LEU* 2.9 37.0 + - + +
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Residues in contact with GLU 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714I ASP* 5.2 0.7 - - - +
808I ARG* 2.7 43.5 + - - -
816I LYS 4.1 0.7 - - - +
817I PRO* 3.6 13.5 - - + +
818I GLY* 3.2 30.3 + - - +
819I VAL 4.1 1.7 + - - -
303L TYR* 3.9 21.3 - - + -
316L ALA 2.9 18.8 + - - +
317L LYS* 3.7 31.1 + - - +
319L VAL* 1.3 78.6 - - - +
321L GLU* 1.3 56.9 + - - +
323L LEU* 3.4 3.3 + - - +
324L LYS* 2.9 26.7 + - - +
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Residues in contact with GLU 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818I GLY* 6.2 1.1 - - - -
35J ARG* 5.6 5.6 + - - +
317L LYS* 2.9 26.0 + - + +
318L ARG* 3.0 13.2 + - + +
320L GLU* 1.3 72.6 - - - +
322L THR* 1.3 63.3 + - + +
324L LYS* 2.8 38.1 + - - +
325L ILE* 3.0 31.7 + - + +
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Residues in contact with THR 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279L MET* 4.4 23.6 - - - -
282L THR* 4.9 5.8 - - - +
283L ILE* 4.5 9.9 - - - +
286L LEU* 3.1 25.4 - - - +
314L TRP* 4.2 9.2 - - + -
318L ARG* 2.9 26.3 + - + +
319L VAL* 3.1 13.9 + - - -
321L GLU* 1.3 78.3 - - + +
323L LEU* 1.3 55.1 + - - +
325L ILE* 3.3 12.5 + - + +
326L ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817I PRO* 3.9 19.0 - - + +
286L LEU* 5.2 2.7 - - + +
303L TYR* 3.6 29.8 - - + +
319L VAL* 2.9 24.6 + - + +
320L GLU 3.4 6.1 - - - +
322L THR* 1.3 75.5 + - - +
324L LYS* 1.3 63.6 + - - +
326L ALA* 3.2 22.3 + - + +
327L GLN* 3.8 7.5 + - - +
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Residues in contact with LYS 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713I ARG* 3.1 31.4 - - - +
714I ASP 3.2 15.5 + - - +
716I LYS* 3.8 24.8 - - - +
817I PRO* 4.1 21.7 - - - +
818I GLY* 4.3 15.5 - - - -
533J GLY* 4.6 11.2 - - - -
320L GLU 2.9 13.0 + - - +
321L GLU* 2.8 25.7 + - - +
323L LEU* 1.3 77.9 - - - +
325L ILE* 1.3 62.8 + - + +
327L GLN* 3.2 34.3 + - - +
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Residues in contact with ILE 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J TYR* 3.4 42.6 - - + +
35J ARG* 3.9 25.4 - - - +
271L ARG* 5.1 0.2 - - - -
273L ILE* 4.6 9.6 - - + +
275L ILE* 5.1 8.6 - - + +
279L MET* 3.9 24.0 - - + -
283L ILE* 5.4 0.4 - - - +
321L GLU* 3.0 33.3 + - + +
322L THR* 3.8 11.0 - - + +
323L LEU 3.3 0.2 - - - -
324L LYS* 1.3 77.5 - - + +
326L ALA* 1.3 65.6 + - - +
327L GLN 3.3 8.4 + - - +
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Residues in contact with ALA 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271L ARG* 3.6 23.0 + - - +
283L ILE* 4.3 27.8 - - + -
322L THR 2.9 13.6 + - - +
323L LEU* 3.2 22.0 - - + +
324L LYS 3.2 0.4 - - - -
325L ILE* 1.3 78.4 - - - +
327L GLN* 1.3 63.0 + - - +
328L GLU* 3.6 2.9 + - - +
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Residues in contact with GLN 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816I LYS* 5.7 4.2 - - - +
817I PRO* 5.8 4.6 + - - +
532J GLY 5.8 0.2 + - - -
533J GLY 3.7 23.8 + - - -
534J ARG* 4.5 22.9 + - - +
535J PHE 5.5 0.4 - - - +
271L ARG* 5.0 0.2 - - - -
273L ILE* 4.3 10.7 - - - +
323L LEU* 3.8 5.7 + - - +
324L LYS* 3.2 30.5 + - - +
325L ILE 3.5 7.4 - - - +
326L ALA* 1.3 81.2 - - - +
328L GLU* 1.3 68.6 + - - +
329L PRO* 4.5 0.2 - - - +
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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
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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