Contacts of the helix formed by residues 499 - 509 (chain A) in PDB entry 3L9X
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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A PRO* 5.7 1.3 - - - +
497A ALA* 3.4 1.5 - - - +
498A ARG* 1.3 92.3 - - - +
500A VAL* 1.3 59.8 + - - +
501A ASP* 3.4 11.3 + - - +
502A HIS* 2.9 35.2 + - - +
503A TYR* 2.9 27.5 + - - +
516A ARG* 4.0 13.2 - - - +
409B ARG* 3.9 21.6 - - + +
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Residues in contact with VAL 500 (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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499A ASP* 1.3 74.2 - - - +
501A ASP* 1.3 65.5 + - - +
503A TYR* 3.3 7.3 + - - +
504A ILE* 2.9 46.0 + - + +
516A ARG* 4.1 18.6 - - - +
555A VAL* 3.9 35.2 - - + -
558A MET* 4.4 14.4 - - + -
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Residues in contact with ASP 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASP* 3.4 11.3 + - - +
500A VAL* 1.3 80.5 - - - +
502A HIS* 1.3 57.7 + - - +
504A ILE* 3.3 16.1 + - - +
505A ARG* 3.1 53.5 + - - +
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Residues in contact with HIS 502 (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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471A ILE 4.9 2.2 - - - -
472A ASP 5.0 1.1 - - - -
474A PRO* 3.6 33.8 + - + +
477A ASN* 3.0 40.1 + - + -
478A LEU* 3.8 21.8 - - + +
496A ARG* 3.6 12.8 - - + -
497A ALA* 3.4 3.1 - - - -
498A ARG* 2.9 26.2 + - + +
499A ASP* 2.9 22.4 + - - +
501A ASP* 1.3 73.0 - - - +
503A TYR* 1.3 66.0 + - - +
505A ARG* 3.1 8.4 + - - +
506A LEU* 2.9 30.4 + - + +
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Residues in contact with TYR 503 (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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497A ALA* 3.6 13.0 - - + +
499A ASP 2.9 14.1 + - - +
500A VAL* 3.4 9.4 - - - +
502A HIS* 1.3 76.6 - - - +
504A ILE* 1.3 65.9 + - - +
506A LEU* 3.4 2.3 + - - +
507A ARG* 3.0 36.4 + - + +
512A GLU 5.2 0.7 + - - -
513A LYS* 5.1 2.4 - - - -
514A PRO* 3.4 43.4 - - + +
516A ARG* 4.0 27.4 - - + -
552A ILE* 4.8 8.7 + - + +
555A VAL* 3.2 38.5 - - + +
556A GLU* 2.3 40.4 + - - +
559A ALA* 4.6 0.9 - - + -
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Residues in contact with ILE 504 (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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500A VAL* 2.9 43.0 + - + +
501A ASP* 3.5 15.0 - - - +
502A HIS 3.2 0.4 - - - -
503A TYR* 1.3 78.4 - - + +
505A ARG* 1.3 59.6 + - + +
507A ARG* 3.2 6.0 + - - +
508A GLN* 2.9 55.0 + - - +
555A VAL 4.6 2.2 - - - +
558A MET* 3.9 28.5 - - + +
559A ALA* 4.0 20.6 - - + +
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Residues in contact with ARG 505 (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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478A LEU* 3.8 34.9 - - + +
501A ASP* 3.1 42.6 + - - +
502A HIS* 3.1 8.2 + - - +
504A ILE* 1.3 78.9 - - + +
506A LEU* 1.3 56.2 + - - +
508A GLN* 3.4 13.3 + - - +
509A ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 506 (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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477A ASN* 3.4 17.7 - - - +
478A LEU* 4.0 11.0 - - + -
481A THR* 3.5 20.6 - - - +
495A ALA* 3.8 18.4 - - + -
496A ARG 3.2 26.7 - - - +
497A ALA* 3.8 18.8 - - + -
502A HIS* 2.9 28.2 + - + +
503A TYR 3.7 3.4 - - - +
505A ARG* 1.3 73.4 - - - +
507A ARG* 1.3 65.8 + - - +
509A ALA* 3.0 13.4 + - - +
510A GLY 3.1 0.3 + - - -
511A VAL* 3.1 28.8 + - + +
514A PRO* 3.8 13.7 - - + -
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Residues in contact with ARG 507 (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 TYR* 3.0 36.6 + - + +
504A ILE 3.5 7.9 - - - +
506A LEU* 1.3 74.3 - - - +
508A GLN* 1.3 57.4 + - + +
510A GLY* 3.0 21.8 + - - -
511A VAL 3.1 27.9 + - - +
512A GLU* 3.5 24.9 + - - +
514A PRO* 3.5 12.1 - - + +
556A GLU* 2.8 36.3 + - - +
559A ALA* 4.1 14.9 - - + +
560A MET* 4.4 20.4 - - + +
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Residues in contact with GLN 508 (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 ILE* 2.9 36.3 + - - +
505A ARG* 3.6 12.4 - - - +
506A LEU 3.2 0.2 - - - -
507A ARG* 1.3 76.4 - - + +
509A ALA* 1.3 57.3 + - - +
510A GLY 3.2 1.1 + - - -
558A MET 5.0 0.2 + - - -
559A ALA 2.9 28.6 + - - +
560A MET* 5.1 2.6 + - + -
561A VAL 4.9 7.5 - - - -
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Residues in contact with ALA 509 (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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478A LEU* 4.8 6.5 - - + -
481A THR* 4.0 21.5 - - + +
482A GLU* 4.9 14.6 - - + +
485A LYS* 3.7 25.2 - - + +
505A ARG 2.9 14.4 + - - +
506A LEU* 3.0 10.9 + - - +
508A GLN* 1.3 73.7 - - - +
510A GLY* 1.3 58.0 + - - +
511A VAL 3.5 0.7 - - - -
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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