Contacts of the helix formed by residues 445 - 460 (chain A) in PDB entry 1L9N
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 SER 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A TYR* 3.9 0.2 - - - +
442A PRO* 2.6 39.5 + - - +
443A GLU 3.4 0.4 - - - -
444A GLY* 1.3 82.9 - - - +
446A ASP* 1.3 65.9 + - - +
447A GLN* 3.2 19.2 + - - +
448A GLU* 3.2 27.7 + - - +
449A ARG* 3.6 5.9 + - - +
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Residues in contact with ASP 446 (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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444A GLY 4.1 2.1 + - - +
445A SER* 1.3 73.1 - - - +
447A GLN* 1.3 63.9 + - - +
449A ARG* 3.2 9.2 + - - +
450A GLN* 2.8 47.6 + - + +
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Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.3 35.7 - - + -
442A PRO* 6.0 1.2 - - - +
445A SER* 3.1 13.7 - - - +
446A ASP* 1.3 86.1 + - - +
448A GLU* 1.3 61.3 + - - +
450A GLN* 2.9 18.6 + - - +
451A VAL* 2.8 35.4 + - + +
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Residues in contact with GLU 448 (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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393A ASN* 3.3 19.9 + - - +
416A HIS* 4.2 7.4 + - - -
440A LYS* 5.5 1.1 - - + -
441A TYR* 3.6 31.3 - - + +
442A PRO 3.3 18.2 - - - +
443A GLU* 3.2 12.3 - - - +
444A GLY 4.1 5.4 - - - +
445A SER* 3.2 10.9 + - - +
447A GLN* 1.3 78.6 - - - +
449A ARG* 1.3 99.1 + - - +
451A VAL* 3.5 7.1 + - - +
452A PHE* 2.9 28.9 + - - +
700A CA 2.9 23.7 - - - -
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Residues in contact with ARG 449 (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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395A ASP* 3.4 27.5 + - - -
415A SER* 3.4 21.8 - - - -
416A HIS* 5.7 1.8 - - - -
445A SER 3.6 6.7 + - - +
446A ASP* 3.2 11.2 + - - +
447A GLN 3.0 0.8 - - - -
448A GLU* 1.3 118.2 + - - +
450A GLN* 1.3 64.6 + - - +
452A PHE* 3.4 39.9 + - - +
453A GLN* 3.1 22.9 + - - +
700A CA 4.0 4.9 - - - -
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ASP* 2.8 47.0 + - + +
447A GLN* 2.9 20.5 + - - +
449A ARG* 1.3 74.1 - - - +
451A VAL* 1.3 61.8 + - + +
453A GLN* 3.4 10.6 + - - +
454A LYS* 2.9 28.3 + - - +
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Residues in contact with VAL 451 (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 ARG 3.4 9.4 - - - +
376A GLU* 3.3 34.8 - - - +
377A GLY* 3.4 7.1 - - - +
389A PHE* 4.0 12.1 - - + -
393A ASN* 6.1 0.2 - - - +
441A TYR* 3.6 31.4 - - + -
447A GLN* 2.8 20.7 + - + +
448A GLU* 3.7 6.1 - - - +
450A GLN* 1.3 76.5 - - + +
452A PHE* 1.3 54.5 + - - +
454A LYS* 3.0 10.3 + - + +
455A ALA* 2.7 34.1 + - - +
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Residues in contact with PHE 452 (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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305A ASN 4.8 1.3 - - - -
306A LEU* 3.4 40.0 - - + +
307A SER* 5.8 0.7 - - - -
389A PHE* 4.3 15.9 - + - -
393A ASN* 3.4 30.1 - - - +
395A ASP* 3.2 28.3 - - + -
448A GLU 2.9 18.5 + - - +
449A ARG* 3.4 31.4 - - - +
451A VAL* 1.3 76.7 - - - +
453A GLN* 1.3 56.4 + - - +
455A ALA* 3.2 2.4 + - - +
456A LEU* 2.8 56.0 + - + +
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Residues in contact with GLN 453 (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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449A ARG 3.1 14.1 + - - +
450A GLN* 3.6 9.6 - - - +
452A PHE* 1.3 82.4 - - + +
454A LYS* 1.3 54.1 + - - +
456A LEU* 3.3 7.7 + - + +
457A GLY* 2.7 33.8 + - - -
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Residues in contact with LYS 454 (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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376A GLU* 3.1 28.4 + - - +
377A GLY 4.2 1.3 - - - +
378A ASP* 2.6 32.5 + - - -
450A GLN 2.9 15.9 + - - +
451A VAL* 3.2 11.0 - - + +
453A GLN* 1.3 78.4 - - - +
455A ALA* 1.3 61.8 + - - +
457A GLY* 3.3 1.7 + - - -
458A LYS* 3.1 47.1 + - - +
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Residues in contact with ALA 455 (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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306A LEU* 3.7 15.5 - - + -
377A GLY* 3.8 18.2 - - - +
379A VAL* 3.7 15.3 - - + +
389A PHE* 3.9 18.4 - - + -
451A VAL 2.7 18.8 + - - +
452A PHE 3.6 4.0 - - - +
454A LYS* 1.3 70.1 - - - +
456A LEU* 1.3 66.4 + - - +
458A LYS* 3.1 6.4 + - - +
459A LEU* 3.1 24.3 + - - +
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Residues in contact with LEU 456 (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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305A ASN* 3.5 37.9 - - + +
306A LEU* 3.5 11.4 - - + +
452A PHE* 2.8 38.8 + - + +
453A GLN* 3.7 6.7 - - + +
455A ALA* 1.3 69.3 - - - +
457A GLY* 1.3 62.7 + - - +
459A LEU* 2.8 7.1 + - + +
460A LYS* 2.7 45.7 + - + +
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Residues in contact with GLY 457 (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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453A GLN 2.7 21.6 + - - -
454A LYS* 3.7 2.5 - - - -
455A ALA 3.3 0.2 - - - -
456A LEU* 1.3 74.0 - - - +
458A LYS* 1.3 61.4 + - - +
460A LYS* 3.4 21.4 - - - +
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Residues in contact with LYS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY 3.5 24.7 - - - +
378A ASP* 4.4 1.4 + - - -
379A VAL* 3.8 12.8 - - + -
380A GLN* 3.4 46.9 - - + +
454A LYS* 3.1 38.6 + - - +
455A ALA 3.1 7.5 + - - +
456A LEU 3.1 0.4 - - - -
457A GLY* 1.3 77.9 - - - +
459A LEU* 1.3 62.3 + - - +
460A LYS 3.6 2.3 + - - +
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Residues in contact with LEU 459 (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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304A ARG* 3.5 43.5 - - + +
306A LEU* 3.4 38.4 - - + -
379A VAL* 4.2 11.0 - - + +
386A PRO* 3.6 38.1 - - + -
455A ALA 3.1 10.5 + - - +
456A LEU* 2.8 9.2 + - + +
458A LYS* 1.3 78.1 - - - +
460A LYS* 1.3 71.7 + - + +
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Residues in contact with LYS 460 (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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303A ASP 3.7 14.5 + - - -
304A ARG* 3.4 25.6 + - - +
305A ASN* 4.0 13.3 - - - +
456A LEU* 2.7 27.5 + - + +
457A GLY* 3.4 17.9 - - - +
458A LYS 4.5 1.7 - - - +
459A LEU* 1.3 91.6 + - + +
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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