Contacts of the helix formed by residues 473 - 485 (chain I) in PDB entry 1MKD
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 ILE 473 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370I MET* 3.7 26.7 - - + -
373I HIS* 3.6 35.3 + - + +
374I MET* 4.5 10.3 - - + -
416I LEU* 3.9 14.8 - - + -
469I PHE* 3.0 33.0 + - + +
471I ASP 3.7 0.4 - - - -
472I TYR* 1.3 95.0 - - + +
474I VAL* 1.3 66.6 + - - +
476I PRO* 3.2 5.7 - - - +
477I LEU* 3.1 24.5 + - - +
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Residues in contact with VAL 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I LEU* 3.7 18.2 - - + +
419I PRO* 4.1 10.5 - - + -
420I THR* 4.4 1.3 - - + -
469I PHE* 3.1 49.1 + - + +
470I ILE* 3.9 9.2 - - - -
473I ILE* 1.3 74.4 - - + +
475I HIS* 1.3 59.9 + - - +
477I LEU* 3.3 5.9 + - - +
478I TRP* 2.9 52.1 + - + +
496I LEU* 3.8 20.6 - - + -
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Residues in contact with HIS 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470I ILE* 2.7 36.6 + - + +
471I ASP* 4.7 4.7 - - - +
474I VAL* 1.3 73.2 - - - +
476I PRO* 1.3 66.9 - - + +
479I GLU* 2.8 67.8 + - + +
493I LEU* 3.6 12.9 - - + +
496I LEU* 3.7 14.5 - - + +
497I GLU* 3.1 40.6 + - + -
500I ARG* 6.2 2.9 - - - -
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Residues in contact with PRO 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I LEU* 3.8 19.0 - - + +
381I LYS* 5.0 5.6 - - - +
470I ILE 3.3 2.9 - - - +
471I ASP 3.2 27.8 - - - +
472I TYR* 3.6 13.7 - - - +
473I ILE 3.2 12.6 - - - +
475I HIS* 1.3 92.6 - - + +
477I LEU* 1.3 54.8 + - - +
479I GLU* 3.8 12.6 - - - +
480I THR* 2.8 31.7 + - - -
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Residues in contact with LEU 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I HIS* 3.9 8.3 - - + -
377I LEU* 3.8 18.8 - - + +
380I LEU* 4.4 4.9 - - + -
409I ASN* 4.3 14.8 - - - +
412I HIS* 3.5 35.0 - - + +
413I CYS* 3.8 34.1 - - - -
416I LEU* 3.8 22.7 - - + -
473I ILE 3.1 17.9 + - - +
474I VAL* 3.6 2.5 - - - +
476I PRO* 1.3 76.5 - - - +
478I TRP* 1.3 63.1 + - + +
480I THR* 3.1 6.2 + - - -
481I TRP* 2.9 24.1 + - - +
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Residues in contact with TRP 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 3.8 24.9 - + - -
272I LEU* 4.0 9.0 - - + -
413I CYS* 3.3 41.0 + - + +
416I LEU 3.2 18.8 + - - -
417I SER* 4.0 12.3 - - - -
420I THR* 3.6 15.4 - - + +
474I VAL* 2.9 44.7 + - + +
477I LEU* 1.3 77.7 - - + +
479I GLU* 1.3 56.8 + - - +
481I TRP* 3.7 31.6 - + - +
482I ALA* 2.7 35.8 + - + +
489I ALA* 5.0 3.8 - - + -
492I ILE* 3.8 27.4 - - + -
493I LEU* 4.4 8.8 - - + +
496I LEU* 4.0 13.9 - - + -
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Residues in contact with GLU 479 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475I HIS* 2.8 47.1 + - + +
476I PRO* 3.8 10.0 - - - +
478I TRP* 1.3 76.2 - - - +
480I THR* 1.3 64.6 + - - +
482I ALA* 3.3 3.1 + - - +
483I ASP* 3.1 33.3 + - - +
493I LEU* 4.3 18.0 - - + +
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Residues in contact with THR 480 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I LEU* 3.4 13.2 - - + +
380I LEU* 3.4 27.6 - - + -
381I LYS* 3.8 30.7 - - + +
384I VAL* 3.7 17.0 - - + +
476I PRO 2.8 17.9 + - - -
477I LEU 3.1 8.4 + - - -
479I GLU* 1.3 80.9 - - - +
481I TRP* 1.3 62.3 + - - +
483I ASP* 3.0 22.6 + - - +
484I LEU* 3.1 5.9 + - - +
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Residues in contact with TRP 481 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LEU* 4.1 23.0 - - + +
275I THR* 5.0 2.7 - - + +
278I LEU* 4.2 5.8 - - + -
380I LEU* 4.1 8.9 - - + +
406I VAL* 3.8 32.1 - - + -
409I ASN* 4.4 10.5 - - + -
410I MET* 3.8 45.1 - - + -
413I CYS* 3.8 27.1 - - - -
477I LEU 2.9 16.2 + - - +
478I TRP* 3.3 26.7 + + + +
480I THR* 1.3 75.6 - - - +
482I ALA* 1.3 63.5 + - - +
484I LEU* 3.1 29.6 + - + +
485I VAL* 3.1 47.1 + - + +
489I ALA* 4.2 5.5 - - + +
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Residues in contact with ALA 482 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478I TRP* 2.7 22.1 + - + +
479I GLU 3.5 6.3 - - - +
481I TRP* 1.3 73.6 - - - +
483I ASP* 1.3 57.2 + - - +
485I VAL* 3.6 0.7 - - - +
486I HIS* 2.9 35.3 + - + +
487I PRO* 4.6 2.1 - - - +
489I ALA* 3.7 29.3 - - + +
490I GLN* 5.2 2.9 - - - +
493I LEU* 3.8 25.6 - - + -
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Residues in contact with ASP 483 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384I VAL* 3.5 25.1 - - + +
387I LYS* 3.1 18.5 + - - -
479I GLU* 3.1 23.3 + - - +
480I THR* 3.0 14.7 + - - +
482I ALA* 1.3 77.8 - - - +
484I LEU* 1.3 66.5 + - - +
486I HIS* 3.2 18.9 + - - +
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Residues in contact with LEU 484 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ALA* 4.8 0.7 - - - +
278I LEU* 5.6 0.2 - - + -
380I LEU* 4.2 14.4 - - + -
383I MET* 4.3 28.9 - - + +
384I VAL* 4.1 18.1 - - + +
387I LYS* 3.7 19.0 + - + +
395I LEU* 3.7 45.3 - - + +
397I LEU* 6.2 0.9 - - + -
406I VAL* 4.3 15.9 - - + -
480I THR 3.1 7.2 + - - +
481I TRP* 3.1 35.6 + - + +
483I ASP* 1.3 80.8 - - - +
485I VAL* 1.3 62.9 + - + +
486I HIS 3.4 0.2 - - - -
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Residues in contact with VAL 485 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I THR* 4.1 17.7 - - + +
277I ALA* 3.7 24.7 - - + -
278I LEU* 4.4 7.4 - - + -
395I LEU* 4.8 1.1 - - + -
481I TRP* 3.2 52.9 - - + +
482I ALA 4.1 0.4 - - - +
484I LEU* 1.3 86.2 - - + +
486I HIS* 1.3 66.1 + - - +
488I ASP* 2.9 25.5 + - + +
489I ALA* 3.8 21.5 - - + +
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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