Contacts of the helix formed by residues 469 - 480 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B ASP* 3.4 44.0 - - + +
326B TYR* 3.9 6.3 - - + -
353B LEU* 3.7 32.1 - - + -
357B LEU* 4.2 1.1 - - + -
417B TRP* 4.4 4.0 - - + -
465B LEU* 2.9 41.2 + - + +
466B GLN 3.6 2.7 - - - -
468B VAL* 1.3 89.3 - - + +
470B PRO* 1.3 58.6 - - - +
471B GLU 3.5 2.0 + - - -
472B SER* 3.7 4.0 + - - -
473B THR* 2.7 35.4 + - + +
509B PHE* 3.9 24.9 - - + -
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Residues in contact with PRO 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 3.7 34.5 - - - +
86B ASN* 3.5 23.3 - - - +
322B ASP* 3.6 11.7 - - - +
325B ARG* 3.6 13.7 - - - +
466B GLN* 3.3 18.2 - - + +
468B VAL 3.6 7.2 - - - +
469B MET* 1.3 86.4 - - - +
471B GLU* 1.3 59.8 + - + +
473B THR* 3.1 14.7 + - - +
474B ALA* 3.2 14.4 + - - +
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Residues in contact with GLU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ASN* 4.2 16.4 - - - +
321B LEU* 3.9 24.0 - - - +
322B ASP* 3.5 10.5 + - - +
470B PRO* 1.3 77.9 - - - +
472B SER* 1.3 64.6 + - - +
474B ALA* 3.4 7.6 + - - +
475B LYS* 3.2 31.6 + - - +
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Residues in contact with SER 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ASP* 2.7 37.5 + - - +
323B GLN* 5.1 2.6 + - - -
469B MET* 4.3 4.3 - - - -
471B GLU* 1.3 73.1 - - - +
473B THR* 1.3 58.3 + - - +
475B LYS* 3.3 8.3 + - - +
476B LEU* 2.9 28.2 + - - +
508B ILE* 3.7 18.0 + - - +
509B PHE* 3.7 33.1 - - - -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B SER* 3.4 30.1 - - - +
465B LEU* 3.6 27.1 - - + +
466B GLN* 3.4 18.7 - - - +
469B MET* 2.7 31.6 + - + +
470B PRO 3.1 9.2 + - - -
472B SER* 1.3 74.6 - - - +
474B ALA* 1.3 59.6 + - - +
476B LEU* 3.7 12.1 - - + +
477B LEU* 2.8 36.4 + - - +
509B PHE* 5.7 1.1 - - + -
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Residues in contact with ALA 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B GLN* 5.4 1.8 - - - +
470B PRO 3.2 15.1 + - - +
471B GLU* 3.5 9.4 - - - +
472B SER 3.3 0.2 - - - -
473B THR* 1.3 82.9 + - - +
475B LYS* 1.3 58.3 + - + +
477B LEU* 4.7 1.8 - - - -
478B ASP* 3.1 33.5 + - - +
487B ARG* 3.2 22.1 + - - +
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Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B GLU* 3.2 17.5 + - - +
472B SER* 3.7 10.1 - - - +
474B ALA* 1.3 77.6 - - + +
476B LEU* 1.3 64.4 + - - +
478B ASP* 3.2 14.6 + - - +
479B LEU* 3.2 26.0 + - - +
508B ILE* 3.9 22.7 - - + -
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B LEU* 4.5 18.4 - - + -
361B ALA* 3.9 25.1 - - + -
365B LEU* 4.7 10.1 - - + -
458B VAL* 4.6 7.6 - - + -
462B SER* 3.2 26.7 - - - +
465B LEU* 6.3 0.7 - - + -
472B SER 2.9 15.5 + - - +
473B THR* 3.7 11.0 - - + +
475B LYS* 1.3 76.9 - - - +
477B LEU* 1.3 60.8 + - - +
479B LEU* 3.4 8.8 + - + +
480B LEU* 3.3 27.7 + - + +
508B ILE* 4.1 21.0 - - + +
509B PHE* 4.3 22.2 - - + -
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ARG* 4.2 6.5 - - + +
462B SER* 3.9 20.2 - - - +
463B LEU* 3.8 31.9 - - + -
466B GLN* 3.6 34.5 - - + +
473B THR 2.8 22.4 + - - +
474B ALA* 4.8 0.2 - - - -
476B LEU* 1.3 74.9 - - - +
478B ASP* 1.3 62.1 + - - +
480B LEU* 3.3 10.0 + - + -
481B GLY 3.3 3.6 + - - -
482B GLN* 3.0 42.9 + - + +
487B ARG* 3.6 29.9 + - - +
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Residues in contact with ASP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B ALA* 3.1 20.5 + - - +
475B LYS* 3.2 18.8 + - - +
477B LEU* 1.3 76.6 - - - +
479B LEU* 1.3 57.3 + - + +
481B GLY* 3.1 15.8 + - - -
482B GLN 5.1 0.9 - - - +
484B THR* 5.4 1.0 + - - -
487B ARG* 2.7 28.1 + - - +
503B PRO* 3.4 21.2 - - + +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLN* 5.5 0.4 - - - +
365B LEU* 3.4 39.0 - - + +
475B LYS 3.2 11.3 + - - +
476B LEU* 3.7 10.3 - - + +
477B LEU 3.3 0.2 - - - -
478B ASP* 1.3 77.7 - - + +
480B LEU* 1.3 59.1 + - - +
481B GLY 3.2 1.5 + - - -
502B LEU* 3.6 17.0 - - - +
503B PRO* 4.0 19.6 - - + +
504B ALA 3.6 23.6 - - - +
505B PRO* 3.9 7.4 - - + -
506B SER* 3.8 21.3 - - - +
508B ILE* 3.8 30.3 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU* 4.3 10.3 - - + -
376B VAL* 4.8 0.7 - - - +
455B LEU* 3.9 45.5 - - + +
458B VAL* 4.0 13.2 - - + -
459B ARG* 3.7 30.5 - - + +
462B SER* 3.9 15.3 - - - +
476B LEU* 3.3 19.6 + - + +
477B LEU* 3.3 11.2 + - + +
478B ASP 3.2 0.8 - - - -
479B LEU* 1.3 77.2 - - - +
481B GLY* 1.3 61.6 + - - +
482B GLN* 3.2 7.3 + - + +
496B ILE* 3.7 25.4 - - + +
500B THR* 5.0 1.4 - - - +
502B LEU* 3.4 15.9 - - - +
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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