Contacts of the helix formed by residues 478 - 492 (chain A) in PDB entry 1MH3
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 SER 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ALA* 3.7 22.9 - - - -
472A ALA 4.6 0.7 - - - -
475A ALA* 4.1 8.1 + - - -
476A ALA 4.1 1.2 - - - -
477A ILE* 1.3 76.8 - - - +
479A PRO* 1.3 70.1 - - - +
480A GLN* 3.4 15.9 + - - +
481A ALA* 3.1 25.1 + - - +
482A ARG* 2.8 27.4 + - - -
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Residues in contact with PRO 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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338A ALA* 5.5 0.7 - - + +
341A TYR* 4.2 10.3 - - + +
472A ALA* 4.0 35.2 - - + +
475A ALA* 5.2 2.2 - - + -
477A ILE 4.5 0.9 - - - +
478A SER* 1.3 89.1 - - - +
480A GLN* 1.3 74.9 + - - +
482A ARG* 3.7 11.5 - - + +
483A ALA* 2.9 30.1 + - - +
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Residues in contact with GLN 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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337A SER 4.8 0.6 - - - +
338A ALA* 4.0 7.3 - - - -
341A TYR* 2.8 72.3 - - + +
478A SER* 3.4 20.9 + - - +
479A PRO* 1.3 86.9 - - - +
481A ALA* 1.3 62.3 + - - +
483A ALA* 3.3 7.7 + - - +
484A PHE* 3.1 21.8 + - - +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ILE* 3.9 13.9 - - + -
478A SER* 3.1 23.8 + - - +
480A GLN* 1.3 78.1 - - - +
482A ARG* 1.3 57.3 + - - +
484A PHE* 3.0 5.7 + - - +
485A LEU* 2.9 32.6 + - - +
507A CYS* 3.8 35.1 - - + +
509A ILE* 5.0 7.9 - - + -
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Residues in contact with ARG 482 (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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475A ALA* 5.4 2.6 - - - +
477A ILE* 2.7 54.2 + - + +
478A SER 2.8 17.6 + - - +
479A PRO* 3.7 9.2 - - - +
481A ALA* 1.3 72.0 - - - +
483A ALA* 1.3 63.2 + - - +
485A LEU* 3.2 8.5 + - - +
486A GLU* 2.9 32.0 + - + +
517A TRP* 4.9 16.5 - - + +
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Residues in contact with ALA 483 (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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479A PRO 2.9 18.9 + - - +
480A GLN* 3.5 8.3 - - - +
482A ARG* 1.3 75.5 - - - +
484A PHE* 1.3 62.3 + - - +
486A GLU* 3.3 7.6 + - - +
487A GLN* 3.0 22.2 + - - +
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Residues in contact with PHE 484 (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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49A GLN* 6.3 3.1 - - + -
480A GLN 3.1 11.1 + - - +
481A ALA* 3.0 9.5 + - - +
483A ALA* 1.3 77.3 - - - +
485A LEU* 1.3 63.7 + - - +
487A GLN* 3.1 11.0 + - + +
488A VAL* 3.1 44.0 + - + +
503A VAL* 3.9 28.9 - - + -
506A LYS* 3.9 34.5 - - + -
507A CYS* 3.8 24.7 - - + -
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Residues in contact with LEU 485 (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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477A ILE* 4.2 23.8 - - + -
481A ALA 2.9 18.8 + - - +
482A ARG* 3.5 7.6 - - - +
484A PHE* 1.3 77.4 - - - +
486A GLU* 1.3 57.0 + - - +
488A VAL* 3.3 6.2 + - - +
489A PHE* 2.8 28.6 + - - +
503A VAL* 3.9 26.2 - - + -
507A CYS* 4.3 9.0 - - - -
509A ILE* 5.0 5.2 - - + -
514A VAL* 4.5 12.6 - - + -
517A TRP* 3.6 48.6 - - + +
518A PHE* 4.1 17.9 - - + -
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Residues in contact with GLU 486 (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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482A ARG* 2.9 26.5 + - + +
483A ALA* 3.7 7.6 - - - +
485A LEU* 1.3 74.2 - - - +
487A GLN* 1.3 61.4 + - - +
489A PHE* 3.7 9.5 - - - +
490A ARG* 2.9 31.5 + - - +
517A TRP* 3.7 17.4 - - + -
521A LYS* 2.7 37.7 + - - -
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Residues in contact with GLN 487 (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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483A ALA 3.0 13.3 + - - +
484A PHE* 3.1 16.6 + - + +
486A GLU* 1.3 77.3 - - - +
488A VAL* 1.3 66.1 + - + +
490A ARG* 3.5 11.9 + - - +
491A ARG* 3.6 10.7 + - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 3.1 42.7 + - + +
485A LEU* 3.6 7.4 - - - +
487A GLN* 1.3 75.1 - - + +
489A PHE* 1.3 61.3 + - - +
491A ARG* 2.9 7.8 + - - +
492A LYS* 2.8 28.5 + - + +
495A LEU* 4.0 24.0 - - + -
503A VAL* 4.4 11.2 - - + -
518A PHE* 3.9 19.3 - - + -
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Residues in contact with PHE 489 (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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485A LEU 2.8 16.3 + - - +
486A GLU* 3.7 9.6 - - - +
488A VAL* 1.3 76.4 - - - +
490A ARG* 1.3 65.0 + - - +
491A ARG 3.2 0.7 + - - -
492A LYS 3.3 18.4 + - - -
493A GLN* 3.3 71.5 + - + +
517A TRP* 3.8 13.9 - + + -
518A PHE* 3.8 17.0 - + + -
521A LYS* 3.6 46.7 - - + -
522A ARG* 4.0 14.1 - - + -
524A ARG* 6.3 0.2 - - - -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU* 2.9 17.9 + - - +
487A GLN* 3.6 9.2 - - - +
488A VAL 3.2 0.2 - - - -
489A PHE* 1.3 79.3 - - - +
491A ARG* 1.3 57.6 + - - +
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Residues in contact with ARG 491 (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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487A GLN 3.6 8.0 + - - +
488A VAL* 2.9 9.0 + - - +
489A PHE 4.0 0.2 - - - -
490A ARG* 1.3 81.5 - - - +
492A LYS* 1.3 63.3 + - + +
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Residues in contact with LYS 492 (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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488A VAL* 2.8 18.1 + - + +
489A PHE* 3.3 10.3 + - - -
491A ARG* 1.3 82.2 - - + +
493A GLN* 1.3 61.9 + - - +
494A SER* 2.9 33.4 + - - +
495A LEU* 4.0 15.0 - - + +
496A ASN* 5.2 1.4 + - - -
499A GLU* 2.8 34.0 + - - +
518A PHE* 3.5 8.5 - - - -
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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