Contacts of the helix formed by residues 473 - 497 (chain C) in PDB entry 2MSD
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 LYS 473 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A LEU* 3.6 36.6 - - + -
304A GLU* 3.0 22.6 + - - -
305A MET* 3.0 48.0 - - - +
469C LEU* 2.9 35.5 + - + +
470C TYR* 3.3 10.7 + - + +
471C ARG 3.3 0.4 - - - -
472C GLN* 1.3 85.2 - - - +
474C VAL* 1.3 64.4 + - + +
475C GLU 3.3 0.7 - - - -
476C PRO* 3.2 3.5 - - - +
477C LEU* 2.8 43.2 + - + +
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Residues in contact with VAL 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C TYR* 2.6 48.9 + - + +
473C LYS* 1.3 76.3 - - + +
475C GLU* 1.3 52.9 + - + +
477C LEU* 3.6 7.9 - - + +
478C ARG* 2.7 54.4 + - + +
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Residues in contact with GLU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C TYR 3.3 1.6 + - - +
471C ARG* 3.2 41.7 - - + +
474C VAL* 1.3 78.9 - - + +
476C PRO* 1.4 63.6 - - + +
478C ARG* 3.1 24.9 + - - +
479C ALA* 3.3 7.3 + - - +
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Residues in contact with PRO 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 3.5 22.7 - - - +
301A LEU* 5.3 0.4 - - + -
471C ARG 3.4 11.9 - - - +
472C GLN* 3.3 20.6 - - - +
473C LYS* 3.2 16.2 - - - +
475C GLU* 1.4 96.3 - - + +
477C LEU* 1.3 53.7 + - - +
479C ALA* 3.0 12.0 + - + +
480C GLU* 2.8 33.6 + - - +
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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
----------------------------------------------------------
294A LEU* 4.4 22.0 - - + -
297A LYS* 4.0 21.5 - - + +
301A LEU* 4.8 9.6 - - + -
473C LYS* 2.8 31.0 + - + +
474C VAL* 3.7 7.9 - - + +
476C PRO* 1.3 74.1 - - - +
478C ARG* 1.3 56.1 + - - +
480C GLU* 3.6 18.8 - - + +
481C LEU* 2.7 51.2 + - + +
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Residues in contact with ARG 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C VAL* 2.7 38.7 + - + +
475C GLU* 3.2 13.7 - - - +
477C LEU* 1.3 77.1 - - - +
479C ALA* 1.3 56.0 + - - +
481C LEU* 4.1 8.0 - - + +
482C GLN* 2.8 45.6 + - - +
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Residues in contact with ALA 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C GLU 3.3 5.5 + - - +
476C PRO* 3.0 14.9 + - + +
478C ARG* 1.3 79.1 - - - +
480C GLU* 1.3 61.3 + - - +
482C GLN* 3.4 7.8 - - - +
483C GLU* 2.9 39.8 + - - +
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Residues in contact with GLU 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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293A GLU* 4.0 35.0 - - + +
294A LEU* 5.9 3.1 - - + -
297A LYS* 2.6 49.4 + - - +
476C PRO* 2.8 24.9 + - - +
477C LEU* 3.6 16.9 - - + +
479C ALA* 1.3 78.6 - - - +
481C LEU* 1.3 57.8 + - + +
483C GLU* 3.4 4.7 + - - +
484C GLY* 2.8 26.5 + - - -
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Residues in contact with LEU 481 (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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294A LEU* 4.9 17.7 - - + -
477C LEU* 2.7 37.2 + - + +
478C ARG* 4.1 7.4 - - + +
480C GLU* 1.3 73.4 - - + +
482C GLN* 1.3 56.3 + - - +
484C GLY* 4.3 2.0 - - - +
485C ALA* 2.7 36.3 + - - +
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Residues in contact with GLN 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ARG* 2.8 37.4 + - - +
479C ALA* 3.2 9.7 + - - +
481C LEU* 1.3 74.4 - - - +
483C GLU* 1.3 55.3 + - - +
485C ALA* 3.2 5.7 + - - +
486C ARG* 2.7 76.4 + - + +
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Residues in contact with GLU 483 (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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289A GLN* 6.1 3.4 - - - +
479C ALA* 2.9 26.0 + - - +
480C GLU* 3.8 5.2 - - - +
482C GLN* 1.3 77.8 - - - +
484C GLY* 1.3 58.4 + - - +
486C ARG* 2.7 42.1 + - - +
487C GLN* 2.8 35.4 + - + +
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Residues in contact with GLY 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 6.0 2.7 - - - -
290A LYS* 3.6 27.1 - - - -
480C GLU 2.8 17.4 + - - -
481C LEU* 3.7 2.9 - - - -
483C GLU* 1.3 78.0 - - - +
485C ALA* 1.3 56.3 + - - +
487C GLN* 3.4 5.9 + - - +
488C LYS* 2.8 28.6 + - - +
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Residues in contact with ALA 485 (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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481C LEU 2.7 23.7 + - - +
482C GLN* 3.6 5.8 - - - +
484C GLY* 1.3 70.4 - - - +
486C ARG* 1.3 57.2 + - + +
488C LYS* 3.2 7.4 + - - +
489C LEU* 2.6 48.2 + - + +
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Residues in contact with ARG 486 (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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482C GLN* 2.7 55.0 + - + +
483C GLU* 2.7 48.8 + - - +
485C ALA* 1.3 72.9 - - + +
487C GLN* 1.3 58.5 + - - +
489C LEU* 3.4 14.0 + - + +
490C HIS* 2.8 28.4 + - - +
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Residues in contact with GLN 487 (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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286A GLY* 5.7 3.1 - - - -
289A GLN* 3.9 22.3 - - - +
290A LYS* 4.2 6.3 - - - -
483C GLU* 2.8 20.2 + - + +
484C GLY* 3.5 6.5 - - - +
486C ARG* 1.3 77.6 - - - +
488C LYS* 1.3 51.7 + - - +
490C HIS* 3.1 13.8 + - - +
491C GLU* 2.7 62.8 + - - +
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Residues in contact with LYS 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.5 9.6 - - + -
290A LYS* 3.8 10.8 - - + +
484C GLY 2.8 18.4 + - - +
485C ALA* 3.2 8.5 + - - +
487C GLN* 1.3 76.0 - - - +
489C LEU* 1.3 53.9 + - + +
491C GLU* 3.2 20.6 + - - +
492C LEU* 2.7 58.5 + - + +
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Residues in contact with LEU 489 (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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65A PCW 5.7 13.0 - - + -
485C ALA* 2.6 36.2 + - + +
486C ARG* 3.6 12.8 - - + +
488C LYS* 1.3 72.0 - - - +
490C HIS* 1.3 53.5 + - - +
492C LEU* 3.2 16.7 + - + +
493C GLN* 2.6 51.2 + - + +
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Residues in contact with HIS 490 (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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486C ARG 2.8 14.9 + - - +
487C GLN* 3.3 17.2 + - - +
489C LEU* 1.3 74.2 - - - +
491C GLU* 1.3 64.9 + - - +
493C GLN* 3.7 16.1 + - + +
494C GLU* 2.9 60.5 + - + +
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Residues in contact with GLU 491 (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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282A GLU* 4.9 20.9 - - + -
283A LEU* 3.7 21.6 - - + +
286A GLY* 4.5 2.8 - - - -
290A LYS* 2.8 34.8 + - - -
487C GLN* 2.7 45.7 + - - +
488C LYS* 3.2 13.1 + - + +
490C HIS* 1.3 79.2 - - - +
492C LEU* 1.3 60.3 + - + +
494C GLU* 3.5 7.2 + - - +
495C LYS* 2.8 47.3 + - - +
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Residues in contact with LEU 492 (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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283A LEU* 6.2 3.6 - - + -
488C LYS* 2.7 50.5 + - + +
489C LEU* 3.6 20.0 - - + +
491C GLU* 1.3 72.9 - - + +
493C GLN* 1.3 54.8 + - + +
495C LYS* 2.9 17.3 + - + +
496C LEU* 2.7 56.6 + - + +
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Residues in contact with GLN 493 (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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489C LEU* 2.6 36.7 + - + +
490C HIS* 3.7 18.1 - - + +
492C LEU* 1.3 73.0 - - + +
494C GLU* 1.3 60.3 + - + +
495C LYS 3.0 4.4 + - - -
496C LEU* 4.4 10.1 - - + +
497C SER* 2.7 32.9 + - - +
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Residues in contact with GLU 494 (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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279A LEU* 5.2 3.1 - - - +
282A GLU* 5.7 6.2 - - - +
490C HIS* 2.9 51.8 + - + +
491C GLU* 3.9 6.9 - - - +
492C LEU 3.2 0.2 - - - -
493C GLN* 1.3 75.6 - - + +
495C LYS* 1.3 64.6 + - + +
497C SER* 4.9 0.7 - - - -
498C PRO* 3.1 21.8 - - - +
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Residues in contact with LYS 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.5 48.0 - - + +
282A GLU* 2.6 29.2 + - - +
283A LEU* 4.6 14.1 - - - +
491C GLU* 2.8 43.9 + - - +
492C LEU* 2.9 19.7 + - + +
494C GLU* 1.3 80.7 - - - +
496C LEU* 1.3 63.6 + - + +
497C SER 3.1 1.8 - - - -
498C PRO* 3.7 2.5 - - - -
499C LEU* 2.9 47.9 + - + +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C LEU* 2.7 42.3 + - + +
493C GLN* 4.4 9.9 - - + +
495C LYS* 1.3 73.3 - - + +
497C SER* 1.3 58.9 + - - +
499C LEU* 5.1 0.2 - - - -
500C GLY* 3.0 25.3 - - - +
504C ARG* 6.1 0.2 - - - -
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Residues in contact with SER 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C GLN* 2.7 21.5 + - - +
494C GLU* 5.2 0.4 - - - -
495C LYS 3.1 1.2 - - - -
496C LEU* 1.3 76.5 - - - +
498C PRO* 1.4 67.2 - - - +
501C GLU* 3.0 38.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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