Contacts of the helix formed by residues 509 - 519 (chain A) in PDB entry 1LMU
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 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A VAL* 3.4 9.5 - - + +
508A GLN* 1.4 77.2 + - - +
510A LYS* 1.3 77.4 + - - +
511A ASP* 2.8 22.0 + - - +
512A LEU* 2.8 38.5 - - + +
513A LYS* 3.0 26.9 + - - +
569A ASP* 5.4 3.4 - - - +
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Residues in contact with LYS 510 (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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508A GLN 3.3 4.9 + - - +
509A ASP* 1.3 75.2 + - - +
511A ASP* 1.3 65.1 + - - +
513A LYS* 3.1 31.6 + - + +
514A LYS* 2.7 68.5 - - + +
517A ARG* 4.8 0.2 - - - +
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Residues in contact with ASP 511 (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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509A ASP* 2.8 19.5 + - - +
510A LYS* 1.3 81.3 - - - +
512A LEU* 1.3 69.1 + - + +
514A LYS* 3.4 9.1 + - - +
515A ILE* 3.2 26.3 + - + +
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Residues in contact with LEU 512 (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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507A VAL* 4.0 12.6 - - + -
509A ASP* 2.8 37.6 + - + +
510A LYS 3.2 0.2 - - - -
511A ASP* 1.3 82.8 - - + +
513A LYS* 1.3 59.2 + - - +
515A ILE* 3.0 4.5 + - + +
516A LEU* 2.8 37.4 + - + +
569A ASP* 3.3 46.0 - - + +
572A ALA* 3.1 32.8 - - + -
573A HIS* 5.4 11.7 - - + +
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Residues in contact with LYS 513 (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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504A ALA* 3.4 42.5 - - + +
505A ARG* 5.0 6.1 - - - +
507A VAL* 4.9 7.2 - - - +
508A GLN 6.0 0.7 - - - +
509A ASP 3.0 15.1 + - - +
510A LYS* 3.1 29.5 + - + +
512A LEU* 1.3 78.1 - - - +
514A LYS* 1.4 50.4 + - - +
516A LEU* 2.5 32.1 - - - +
517A ARG* 3.2 25.2 + - - +
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Residues in contact with LYS 514 (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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510A LYS* 2.7 70.7 + - + +
511A ASP* 3.7 8.5 - - - +
512A LEU 3.1 0.6 - - - -
513A LYS* 1.4 72.2 - - - +
515A ILE* 1.3 60.1 + - + +
516A LEU 2.5 17.6 - - - +
517A ARG* 2.9 46.3 + - - +
518A ALA* 3.6 15.1 + - - +
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Residues in contact with ILE 515 (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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511A ASP* 3.2 15.2 + - + +
512A LEU* 3.0 12.2 + - + +
514A LYS* 1.3 76.1 - - + +
516A LEU* 1.3 68.5 + - + +
518A ALA* 3.9 2.0 - - - +
519A THR* 2.6 30.0 + - - +
572A ALA* 3.3 24.2 - - + +
576A SER* 2.9 48.5 - - - +
580A GLN* 5.2 2.9 - - - +
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Residues in contact with LEU 516 (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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503A ILE* 3.0 38.4 - - + -
504A ALA* 3.9 11.0 - - + -
507A VAL* 3.7 29.6 - - + -
512A LEU* 2.8 22.0 + - + +
513A LYS 2.5 16.4 - - - +
514A LYS 2.5 19.9 - - - +
515A ILE* 1.3 81.2 - - + +
517A ARG* 1.3 59.3 + - - +
519A THR* 4.1 7.0 - - - +
521A GLY* 4.8 11.4 - - - +
522A LEU* 5.5 0.9 - - + -
568A PRO* 5.0 5.8 - - + +
571A THR* 5.0 6.5 - - + +
572A ALA* 4.1 26.9 - - + +
575A GLU* 5.6 1.3 - - + -
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Residues in contact with ARG 517 (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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501A THR 5.5 4.4 + - - -
502A GLY* 6.2 2.2 - - - -
503A ILE* 5.3 0.6 - - - +
504A ALA* 4.6 9.0 - - + +
510A LYS* 5.1 0.2 - - - +
513A LYS* 3.1 31.6 + - - +
514A LYS* 2.9 82.6 + - - +
516A LEU* 1.3 79.9 - - - +
518A ALA* 1.3 76.6 + - + +
519A THR 2.9 2.8 + - - +
520A ASP* 3.8 12.6 + - - +
521A GLY* 4.6 4.2 - - - +
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Residues in contact with ALA 518 (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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514A LYS 3.6 15.3 - - - +
515A ILE* 3.9 2.5 - - - +
516A LEU 2.9 1.2 + - - -
517A ARG* 1.3 86.6 - - + +
519A THR* 1.4 66.0 + - - +
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Residues in contact with THR 519 (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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515A ILE* 2.6 28.3 + - - +
516A LEU* 4.3 5.8 - - - -
517A ARG 2.9 2.4 - - - +
518A ALA* 1.4 83.2 - - - +
520A ASP* 1.3 74.7 + - + +
521A GLY 3.9 8.5 - - - +
575A GLU* 4.0 36.3 - - + +
576A SER* 3.6 17.5 + - - -
579A THR* 4.5 20.1 + - + +
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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