Contacts of the helix formed by residues 469 - 480 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C ASP* 3.5 42.8 - - + +
326C TYR* 3.9 6.5 - - + -
353C LEU* 3.7 26.7 - - + -
357C LEU* 4.4 0.4 - - + -
417C TRP* 4.3 4.5 - - + -
465C LEU* 2.8 46.3 + - + +
466C GLN 3.8 1.1 - - - -
468C VAL* 1.3 85.0 - - + +
470C PRO* 1.3 58.8 - - - +
471C GLU 3.4 2.2 + - - -
472C SER* 3.6 3.0 + - - -
473C THR* 2.7 36.9 + - + +
509C PHE* 3.7 31.6 - - + -
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Residues in contact with PRO 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 3.7 36.6 - - - +
86C ASN* 3.7 20.9 - - - +
322C ASP* 3.6 10.8 - - - +
325C ARG* 3.7 12.6 - - - +
466C GLN* 3.3 19.9 - - + +
468C VAL 3.6 7.6 - - - +
469C MET* 1.3 85.8 - - - +
471C GLU* 1.3 61.1 + - + +
473C THR* 3.1 14.3 + - - +
474C ALA* 3.2 14.6 + - - +
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Residues in contact with GLU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ASN* 4.0 20.7 + - - +
321C LEU* 3.7 25.3 - - - +
322C ASP* 3.6 10.4 + - - +
469C MET 3.5 0.2 - - - -
470C PRO* 1.3 77.9 - - + +
472C SER* 1.3 64.8 + - - +
474C ALA* 3.4 6.5 + - - +
475C LYS* 3.1 37.0 + - - +
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Residues in contact with SER 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C ASP* 2.7 36.4 + - - +
323C GLN* 5.3 2.1 + - - -
469C MET* 4.3 3.1 - - - -
470C PRO 3.5 0.2 - - - -
471C GLU* 1.3 73.9 - - - +
473C THR* 1.3 57.6 + - - +
475C LYS* 3.3 5.3 + - - +
476C LEU* 2.9 24.5 + - - +
508C ILE* 3.4 25.7 + - - +
509C PHE* 3.6 32.5 - - - -
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Residues in contact with THR 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU* 6.3 0.4 - - + -
462C SER* 3.4 32.1 - - - +
465C LEU* 3.7 26.2 - - + +
466C GLN* 3.4 17.2 - - - +
469C MET* 2.7 32.0 + - + +
470C PRO 3.1 8.7 + - - -
472C SER* 1.3 74.5 - - - +
474C ALA* 1.3 55.6 + - - +
476C LEU* 3.8 8.6 - - + +
477C LEU* 2.8 41.2 + - - +
509C PHE* 5.5 2.5 - - + -
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Residues in contact with ALA 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C GLN* 5.3 2.9 - - - +
470C PRO 3.2 15.6 + - - +
471C GLU* 3.5 8.3 - - - +
473C THR* 1.3 81.8 + - - +
475C LYS* 1.3 58.1 + - + +
477C LEU* 4.6 2.5 - - - -
478C ASP* 3.0 37.0 + - - +
487C ARG* 3.3 16.6 + - - +
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Residues in contact with LYS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C GLU* 3.1 23.4 + - - +
472C SER* 3.6 11.0 - - - +
473C THR 3.3 0.2 - - - -
474C ALA* 1.3 75.5 - - + +
476C LEU* 1.3 62.5 + - - +
478C ASP* 3.4 13.3 + - - +
479C LEU* 3.2 26.7 + - - +
508C ILE* 4.6 14.4 - - + -
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Residues in contact with LEU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU* 4.4 18.8 - - + -
361C ALA* 3.9 21.5 - - + -
365C LEU* 4.2 12.8 - - + -
458C VAL* 4.3 8.5 - - + -
462C SER* 3.3 24.9 - - - +
472C SER 2.9 16.6 + - - +
473C THR* 3.3 8.9 + - + +
475C LYS* 1.3 77.0 - - - +
477C LEU* 1.3 57.2 + - - +
479C LEU* 3.3 2.6 + - - +
480C LEU* 3.1 28.5 + - + +
508C ILE* 3.7 27.7 - - + +
509C PHE* 4.3 23.1 - - + -
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Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C ARG* 4.1 12.6 - - + +
462C SER* 3.9 20.6 - - - +
463C LEU* 3.9 31.0 - - + -
466C GLN* 3.8 34.1 - - + +
473C THR 2.8 26.4 + - - +
474C ALA* 3.9 1.1 - - - +
476C LEU* 1.3 70.6 - - - +
478C ASP* 1.3 63.2 + - - +
480C LEU* 3.3 6.3 + - + -
481C GLY 3.1 3.6 + - - -
482C GLN* 3.0 44.7 + - + +
487C ARG* 3.7 27.4 - - - +
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Residues in contact with ASP 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C ALA* 3.0 21.1 + - - +
475C LYS* 3.4 16.5 - - - +
477C LEU* 1.3 77.5 - - - +
479C LEU* 1.3 58.7 + - + +
481C GLY* 3.1 16.6 + - - -
482C GLN 5.1 0.4 - - - +
487C ARG* 2.6 37.6 + - - +
503C PRO* 3.5 19.8 - - + +
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Residues in contact with LEU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C LEU* 3.6 24.0 - - + +
475C LYS 3.2 11.0 + - - +
476C LEU 3.6 7.4 - - - +
477C LEU 3.3 0.4 - - - -
478C ASP* 1.3 80.3 - - + +
480C LEU* 1.3 57.5 + - - +
481C GLY 3.2 0.7 - - - -
502C LEU* 3.5 28.8 - - - +
503C PRO* 4.0 19.8 - - + +
504C ALA 3.6 23.8 - - - +
505C PRO* 4.0 8.1 - - + -
506C SER* 3.7 22.9 - - - +
508C ILE* 3.5 33.7 - - + -
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C LEU* 4.1 9.4 - - + -
376C VAL* 4.8 0.2 - - - +
455C LEU* 3.9 40.6 - - + +
458C VAL* 3.9 21.8 - - + -
459C ARG* 3.7 29.6 - - + -
462C SER* 4.0 9.9 - - - +
476C LEU* 3.1 24.8 + - + +
477C LEU* 3.7 11.4 - - + +
478C ASP 3.2 0.6 - - - -
479C LEU* 1.3 76.2 - - - +
481C GLY* 1.3 61.0 + - - +
482C GLN* 3.2 4.7 + - + +
496C ILE* 3.6 29.3 - - + +
500C THR* 4.8 1.4 - - - +
502C LEU* 3.4 15.6 - - + +
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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