Contacts of the helix formed by residues 405 - 417 (chain A) in PDB entry 1LSH
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 THR 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A SER* 4.3 5.3 + - - -
403A GLN* 3.3 20.1 + - + +
404A ALA* 1.3 75.3 - - - +
406A ARG* 1.3 63.9 + - - +
407A GLU* 3.3 8.9 + - - +
408A SER* 3.2 23.8 + - - +
409A LEU* 3.2 22.2 + - - +
442A TYR* 3.9 13.2 - - - -
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Residues in contact with ARG 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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405A THR* 1.3 75.6 - - - +
407A GLU* 1.3 62.1 + - - +
409A LEU* 3.3 4.5 + - - +
410A SER* 3.0 25.1 + - - +
442A TYR* 3.7 34.3 + - - +
450A PRO* 3.5 18.7 - - - +
452A GLU* 2.9 30.6 + - - +
453A LEU* 3.9 28.2 - - - +
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Residues in contact with GLU 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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371A SER* 4.2 9.4 - - - +
405A THR* 3.3 7.6 + - - +
406A ARG* 1.3 75.3 - - - +
408A SER* 1.3 66.4 + - - +
410A SER* 3.1 18.4 + - - -
411A TYR* 2.8 74.8 + - + +
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Residues in contact with SER 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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371A SER* 3.7 10.2 + - - -
374A LEU* 3.2 16.8 - - - +
402A GLN* 2.8 25.5 + - - -
403A GLN 4.0 4.9 + - - -
404A ALA* 4.1 6.4 - - - -
405A THR* 3.2 32.6 + - - -
407A GLU* 1.3 77.8 - - - +
409A LEU* 1.3 52.9 + - - +
411A TYR* 4.6 0.2 - - - -
412A ALA* 2.8 35.3 + - - +
438A LEU* 4.0 11.0 - - - -
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Residues in contact with LEU 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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404A ALA* 5.2 0.4 - - + -
405A THR 3.2 7.7 + - - +
406A ARG* 3.7 8.7 - - - +
407A GLU 3.2 0.6 - - - -
408A SER* 1.3 76.7 - - - +
410A SER* 1.3 63.4 + - - +
412A ALA* 3.2 2.3 + - - +
413A ARG* 3.0 23.3 + - - +
435A TYR* 3.8 24.3 + - + +
438A LEU* 3.5 31.2 - - + -
439A VAL* 4.0 21.5 - - + +
442A TYR* 3.5 42.0 - - + -
453A LEU* 3.5 35.0 - - + -
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Residues in contact with SER 410 (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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406A ARG 3.0 14.1 + - - -
407A GLU* 3.1 21.1 + - - -
409A LEU* 1.3 75.4 - - - +
411A TYR* 1.3 66.4 + - - +
413A ARG* 3.0 7.4 + - - +
414A GLU* 2.9 36.0 + - - +
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Residues in contact with TYR 411 (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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371A SER* 3.4 37.5 - - - -
372A GLU* 4.7 6.5 + - - -
374A LEU* 3.8 20.5 - - + +
375A LEU* 3.7 46.7 - - + +
378A LYS* 4.4 8.5 - - + +
407A GLU* 2.8 65.6 + - + +
408A SER 4.0 0.4 - - - +
410A SER* 1.3 75.9 - - - +
412A ALA* 1.3 63.6 + - - +
414A GLU* 3.5 22.6 + - - +
415A LEU* 3.0 22.0 + - - +
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Residues in contact with ALA 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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374A LEU* 4.0 5.3 - - + +
399A LEU* 3.8 18.3 - - + +
408A SER 2.8 19.4 + - - +
409A LEU 3.6 3.8 - - - +
410A SER 3.1 0.2 - - - -
411A TYR* 1.3 77.2 - - - +
413A ARG* 1.3 61.6 + - - +
415A LEU* 3.0 21.7 + - - +
416A LEU* 3.1 12.1 + - - +
435A TYR* 3.8 15.0 - - + -
438A LEU* 3.4 24.0 - - + -
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Residues in contact with ARG 413 (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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409A LEU 3.0 13.6 + - - +
410A SER* 3.0 10.5 + - - +
412A ALA* 1.3 72.4 - - - +
414A GLU* 1.3 69.1 + - + +
416A LEU* 3.0 20.8 + - + +
417A ASN* 3.5 40.0 + - - +
435A TYR* 4.2 10.2 - - + +
455A GLN* 5.1 3.8 - - - +
456A PRO* 3.4 53.9 - - + +
459A ASP* 5.2 7.9 + - - +
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Residues in contact with GLU 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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375A LEU* 5.5 0.2 - - - +
378A LYS* 3.3 34.1 + - + +
410A SER* 2.9 26.8 + - - +
411A TYR* 3.9 22.2 - - - +
413A ARG* 1.3 78.6 - - + +
415A LEU* 1.3 62.9 + - - +
417A ASN* 3.0 24.8 + - - +
418A THR* 3.3 10.6 + - - -
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Residues in contact with LEU 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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374A LEU* 4.5 18.4 - - + -
377A LEU* 4.6 4.0 - - + -
378A LYS* 3.6 29.1 - - + +
381A LEU* 3.5 23.6 - - + -
395A VAL* 4.5 18.4 - - + -
399A LEU* 4.7 11.4 - - + -
411A TYR 3.0 11.5 + - - +
412A ALA* 3.0 14.2 + - - +
414A GLU* 1.3 78.9 - - - +
416A LEU* 1.3 62.2 + - + +
417A ASN 3.0 0.2 - - - -
418A THR* 3.0 18.7 + - - +
421A ILE* 3.1 50.9 - - + +
431A ALA* 5.0 3.4 - - + -
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Residues in contact with LEU 416 (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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412A ALA 3.1 11.3 + - - +
413A ARG* 3.0 13.6 + - + +
415A LEU* 1.3 76.6 - - + +
417A ASN* 1.3 58.1 + - - +
418A THR 3.3 1.6 - - - -
421A ILE* 4.9 6.4 - - + +
422A ARG* 3.3 28.6 + - - +
428A ARG* 4.8 3.3 + - + +
431A ALA* 3.4 45.1 - - + +
432A VAL* 3.6 20.6 - - + +
435A TYR* 3.9 32.5 - - + -
456A PRO* 4.8 13.5 - - + -
457A LEU* 5.2 3.6 - - + -
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Residues in contact with ASN 417 (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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413A ARG* 3.5 37.8 + - - +
414A GLU* 3.0 16.7 + - - +
416A LEU* 1.3 79.8 - - - +
418A THR* 1.3 63.0 + - - +
419A SER 3.6 1.9 + - - -
422A ARG* 3.7 19.8 + - - +
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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