Contacts of the helix formed by residues 469 - 480 (chain A) in PDB entry 2X1L
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 MET 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ASP* 3.6 42.0 - - + +
326A TYR* 4.0 6.3 - - + -
353A LEU* 3.7 31.2 - - + -
357A LEU* 4.1 11.2 - - + -
417A TRP* 4.2 4.9 - - + -
465A LEU* 2.8 36.4 + - + +
466A GLN 3.7 0.9 - - - -
468A VAL* 1.3 84.8 - - + +
470A PRO* 1.4 58.5 - - - +
471A GLU 3.5 1.8 - - - -
472A SER* 4.3 3.8 - - - -
473A THR* 2.7 36.3 + - + +
509A PHE* 3.7 26.5 - - + -
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Residues in contact with PRO 470 (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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34A ARG* 3.6 38.4 - - - +
86A ASN* 3.6 21.1 - - - +
321A LEU* 6.3 0.2 - - + -
322A ASP* 3.7 8.1 - - - +
325A ARG* 3.6 16.4 - - - +
466A GLN* 3.3 16.4 - - + +
468A VAL 3.5 8.7 - - - +
469A MET* 1.4 86.6 - - - +
471A GLU* 1.3 57.1 + - + +
473A THR* 3.0 15.3 + - - +
474A ALA* 3.1 17.7 + - - +
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Residues in contact with GLU 471 (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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86A ASN* 4.2 19.7 + - - +
321A LEU* 3.9 23.9 - - - +
322A ASP* 3.5 10.2 + - - +
469A MET 3.5 0.4 - - - -
470A PRO* 1.3 78.1 - - - +
472A SER* 1.3 63.7 + - - +
474A ALA* 3.4 7.4 + - - +
475A LYS* 3.2 36.8 + - - +
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Residues in contact with SER 472 (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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322A ASP* 2.7 35.6 + - - +
323A GLN* 5.3 2.4 + - - -
469A MET* 3.6 4.7 + - - -
471A GLU* 1.3 72.2 - - - +
473A THR* 1.3 59.5 + - - +
475A LYS* 3.5 2.3 + - - -
476A LEU* 3.1 27.7 + - - +
508A ILE* 3.8 25.0 + - - +
509A PHE* 3.6 33.9 - - - -
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Residues in contact with THR 473 (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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357A LEU* 6.4 0.2 - - + -
462A SER* 3.4 30.1 - - - +
465A LEU* 3.6 28.0 - - + +
466A GLN* 3.4 19.1 - - - +
469A MET* 2.7 31.7 + - + +
470A PRO 3.0 9.2 + - - -
472A SER* 1.3 75.3 - - - +
474A ALA* 1.3 58.4 + - - +
476A LEU* 3.7 9.0 - - + +
477A LEU* 2.8 36.7 + - - +
509A PHE* 5.8 0.9 - - + -
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Residues in contact with ALA 474 (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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466A GLN* 5.7 1.8 - - - -
470A PRO 3.1 19.8 + - - +
471A GLU* 3.5 9.4 - - - +
472A SER 3.3 0.4 - - - -
473A THR* 1.3 77.4 + - - +
475A LYS* 1.3 57.3 + - + +
477A LEU* 4.8 1.8 - - - -
478A ASP* 3.1 32.9 + - - +
487A ARG* 3.3 18.3 + - - +
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Residues in contact with LYS 475 (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 GLU* 3.2 23.0 + - - +
472A SER* 3.8 5.2 - - - +
474A ALA* 1.3 74.9 - - + +
476A LEU* 1.3 63.9 + - - +
478A ASP* 3.3 12.7 + - - +
479A LEU* 3.2 27.8 + - + +
508A ILE* 4.1 25.8 - - + -
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Residues in contact with LEU 476 (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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357A LEU* 4.4 18.6 - - + -
361A ALA* 3.9 26.7 - - + -
365A LEU* 4.4 13.9 - - + -
458A VAL* 4.5 7.6 - - + -
462A SER* 3.3 26.9 - - - +
465A LEU* 6.5 0.2 - - + -
472A SER 3.1 16.6 + - - +
473A THR* 3.3 9.1 + - + +
475A LYS* 1.3 76.3 - - - +
477A LEU* 1.3 61.3 + - - +
479A LEU* 3.6 2.6 + - + +
480A LEU* 3.3 29.9 + - + +
508A ILE* 3.6 19.5 - - + +
509A PHE* 4.3 23.8 - - + -
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Residues in contact with LEU 477 (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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459A ARG* 4.2 10.3 - - + +
462A SER* 4.1 20.0 - - - +
463A LEU* 3.8 29.8 - - + -
466A GLN* 3.6 35.4 - - + +
473A THR 2.8 21.3 + - - +
474A ALA* 4.8 0.4 - - - -
476A LEU* 1.3 73.9 - - - +
478A ASP* 1.3 61.8 - - - +
480A LEU* 3.4 5.8 + - + +
481A GLY 3.4 3.1 + - - -
482A GLN* 3.1 43.6 + - + +
487A ARG* 3.5 33.0 + - - +
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Residues in contact with ASP 478 (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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474A ALA* 3.1 19.9 + - - +
475A LYS* 3.3 14.6 + - - +
477A LEU* 1.3 76.9 - - - +
479A LEU* 1.3 63.9 + - + +
481A GLY* 3.2 12.5 + - - -
482A GLN 5.1 0.7 - - - -
487A ARG* 2.6 31.9 + - - +
503A PRO* 3.4 20.0 - - + +
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Residues in contact with LEU 479 (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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362A GLN* 5.6 0.4 - - - +
365A LEU* 3.6 32.0 - - + +
475A LYS* 3.2 13.3 + - + +
476A LEU 3.9 4.3 - - - +
477A LEU 3.3 0.4 - - - -
478A ASP* 1.3 78.5 - - + +
480A LEU* 1.3 59.5 + - - +
481A GLY 3.2 1.1 - - - -
502A LEU* 3.6 22.7 - - - +
503A PRO* 3.9 18.4 - - + +
504A ALA 3.6 24.9 - - - +
505A PRO* 4.0 8.1 - - + -
506A SER* 3.8 24.7 - - - +
508A ILE* 3.7 28.3 - - + -
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Residues in contact with LEU 480 (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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365A LEU* 4.0 23.3 - - + -
376A VAL* 4.8 0.5 - - - +
455A LEU* 3.9 33.2 - - + +
458A VAL* 3.9 20.4 - - + -
459A ARG* 3.7 33.2 - - + -
462A SER* 4.1 8.7 - - - +
476A LEU* 3.3 21.6 + - + +
477A LEU* 3.4 8.0 + - + +
478A ASP 3.2 0.6 - - - -
479A LEU* 1.3 77.3 - - - +
481A GLY* 1.3 61.3 + - - +
482A GLN* 3.2 6.9 + - + +
496A ILE* 3.6 25.8 - - + +
500A THR* 4.8 1.7 - - - +
502A LEU* 3.4 15.1 - - + +
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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