Contacts of the helix formed by residues 403 - 415 (chain A) in PDB entry 1L0N
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 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A GLU* 3.4 15.5 - - - +
354A VAL* 3.7 9.6 - - - -
358A LYS* 4.9 2.7 - - - +
401A GLU 3.4 5.3 + - - +
402A VAL* 1.3 79.7 - - - +
404A ALA* 1.3 67.0 + - - +
405A ARG* 3.1 16.3 + - - +
406A VAL* 3.0 27.9 + - - +
407A VAL* 3.0 18.5 + - - +
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Residues in contact with ALA 404 (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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349A ALA* 3.7 16.3 - - - +
350A THR 4.0 2.9 - - - -
351A GLU* 2.7 42.4 + - - +
354A VAL* 3.7 14.1 - - + +
403A ASP* 1.3 71.6 - - - +
405A ARG* 1.3 65.4 + - - +
407A VAL* 2.9 4.3 + - - +
408A ARG* 2.8 41.1 + - - +
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Residues in contact with ARG 405 (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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403A ASP* 3.1 16.9 + - - +
404A ALA* 1.3 75.0 - - - +
406A VAL* 1.3 70.9 + - - +
408A ARG* 3.1 31.1 + - + +
409A GLU* 2.9 67.8 + - - +
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Residues in contact with VAL 406 (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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269A ALA* 3.8 15.9 - - + -
401A GLU 4.2 10.1 - - - +
402A VAL* 4.3 9.0 - - + -
403A ASP* 3.0 30.6 + - - +
405A ARG* 1.3 84.0 - - + +
407A VAL* 1.3 55.9 + - - +
409A GLU* 2.8 8.8 + - - +
410A VAL* 2.6 52.3 + - + +
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Residues in contact with VAL 407 (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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269A ALA* 4.4 11.2 - - + +
272A VAL* 4.1 11.7 - - + -
273A ALA* 4.2 9.9 - - + +
276A ILE* 5.1 0.9 - - + -
345A LEU* 4.3 10.5 - - + +
349A ALA* 3.9 17.9 - - + -
354A VAL* 3.8 27.1 - - + -
402A VAL* 3.9 12.1 - - + -
403A ASP 3.0 13.3 + - - +
404A ALA 2.9 8.3 + - - +
406A VAL* 1.3 75.1 - - - +
408A ARG* 1.3 57.8 + - - +
410A VAL* 4.9 2.7 - - - -
411A CYS* 2.8 51.9 + - - -
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Residues in contact with ARG 408 (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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345A LEU 3.1 22.7 - - - +
346A CYS* 2.9 12.9 - - - +
347A THR 3.3 21.5 + - - -
349A ALA* 3.7 11.5 + - + +
404A ALA* 2.8 31.6 + - - +
405A ARG* 3.1 49.5 - - + +
407A VAL* 1.3 73.1 - - - +
409A GLU* 1.3 54.9 + - - +
412A SER* 2.5 31.3 + - - -
16K ASN* 3.1 36.5 + - - +
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Residues in contact with GLU 409 (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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405A ARG* 2.9 66.0 + - - +
406A VAL* 2.8 8.2 + - - +
408A ARG* 1.3 79.5 - - - +
410A VAL* 1.3 66.4 + - + +
412A SER* 3.5 4.3 + - - -
413A LYS* 3.2 22.5 + - - +
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Residues in contact with VAL 410 (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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266A ASP* 3.7 42.4 - - + +
269A ALA* 3.8 14.6 - - + -
270A LEU* 3.8 17.0 - - + +
406A VAL* 2.6 38.2 + - + +
407A VAL 4.2 0.7 - - - +
409A GLU* 1.3 73.3 - - + +
411A CYS* 1.3 64.3 + - - +
413A LYS* 3.4 7.6 + - + +
414A TYR* 3.1 34.8 + - + -
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Residues in contact with CYS 411 (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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269A ALA 5.2 0.9 - - - -
270A LEU* 4.7 6.3 - - - -
273A ALA* 3.4 33.4 - - - -
342A TRP 4.9 0.2 - - - +
345A LEU* 4.3 9.6 - - + -
346A CYS* 3.5 24.7 - - - +
407A VAL* 2.8 31.8 + - - +
410A VAL* 1.3 76.3 - - - +
412A SER* 1.3 54.9 + - - +
414A TYR 3.0 1.4 + - - -
415A PHE* 2.6 56.8 + - + +
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Residues in contact with SER 412 (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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346A CYS* 2.8 29.1 + - - +
347A THR* 5.6 0.3 - - - +
408A ARG 2.5 25.5 + - - -
409A GLU* 3.5 6.5 + - - -
410A VAL 3.3 0.2 - - - -
411A CYS* 1.3 77.4 - - - +
413A LYS* 1.3 63.6 + - - +
416A TYR* 3.1 35.8 + - - +
15J ARG* 6.0 2.4 - - - -
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Residues in contact with LYS 413 (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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264A HIS* 4.1 12.5 + - - -
266A ASP* 3.5 18.4 + - - +
409A GLU 3.2 11.5 + - - +
410A VAL* 3.6 10.8 - - + +
412A SER* 1.3 79.3 - - - +
414A TYR* 1.3 85.5 + - + +
418A GLN* 3.3 19.6 - - - +
26E LYS* 4.5 5.5 + - - +
15J ARG* 6.3 0.7 - - - +
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Residues in contact with TYR 414 (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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257A VAL* 3.2 21.0 - - + +
258A GLU 3.7 10.2 - - - +
259A GLY* 4.2 0.7 - - - -
260A PRO* 3.3 34.9 - - + +
264A HIS* 3.7 8.5 + - - -
266A ASP* 2.6 42.6 + - - -
270A LEU* 4.1 15.0 - - + -
320A LEU* 4.2 18.6 - - + -
410A VAL* 3.1 27.4 - - + +
411A CYS 3.0 3.3 + - - +
413A LYS* 1.3 100.0 + - + +
415A PHE* 1.3 63.0 + - + +
418A GLN* 3.4 16.3 - - - +
26E LYS* 3.4 27.7 + - - +
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Residues in contact with PHE 415 (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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257A VAL* 4.0 26.0 - - + -
270A LEU* 4.6 3.4 - - + -
273A ALA* 5.6 1.8 - - + -
274A ASN* 4.5 9.2 - - - -
320A LEU* 3.5 39.3 - - + -
321A GLY* 4.8 0.7 - - - -
342A TRP* 3.3 61.0 - + + -
343A MET* 4.4 7.2 - - + -
346A CYS* 3.7 10.8 - - - -
411A CYS* 2.6 47.5 + - + +
414A TYR* 1.3 75.0 - - + +
416A TYR* 1.3 67.2 + - - +
417A ASP 3.0 3.6 + - - -
418A GLN* 3.2 13.9 + - - +
441A MET* 3.3 15.4 - - + +
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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