Contacts of the helix formed by residues 510 - 523 (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 THR 510 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLN* 5.1 10.0 + - - +
504A ALA* 4.0 0.2 - - - -
509A ILE* 1.3 77.9 - - - +
511A PRO* 1.3 74.0 - - + +
512A LEU* 3.1 30.1 - - + +
513A GLN* 3.0 31.9 + - + +
514A VAL* 3.0 21.8 + - - +
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Residues in contact with PRO 511 (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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500A LYS* 4.9 7.1 - - + +
501A GLU* 5.0 15.0 - - + +
504A ALA* 3.8 19.7 - - + -
505A LYS* 6.1 2.5 - - - +
509A ILE 4.0 3.8 - - - +
510A THR* 1.3 89.7 - - + +
512A LEU* 1.3 58.7 + - + +
514A VAL* 3.4 5.2 + - + +
515A ARG* 3.0 26.6 + - - +
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Residues in contact with LEU 512 (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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510A THR* 3.1 13.5 - - + +
511A PRO* 1.3 76.0 - - + +
513A GLN* 1.3 61.8 + - - +
515A ARG* 3.6 20.3 - - + +
516A VAL* 2.9 43.6 + - + +
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Residues in contact with GLN 513 (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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476A ALA* 3.0 37.1 + - - +
477A ILE* 3.8 9.7 - - + +
509A ILE* 2.7 38.7 - - + +
510A THR* 3.0 31.1 + - + +
512A LEU* 1.3 80.4 - - + +
514A VAL* 1.3 61.8 + - - +
516A VAL* 3.9 3.6 - - - +
517A TRP* 2.9 25.7 + - - +
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Residues in contact with VAL 514 (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* 4.5 7.0 - - + -
495A LEU* 4.5 0.4 - - + -
500A LYS* 4.0 28.0 - - + +
503A VAL* 4.1 15.0 - - + -
504A ALA* 3.7 22.4 - - + +
509A ILE* 3.5 22.4 - - + +
510A THR 3.0 17.9 + - - +
511A PRO 3.5 7.6 - - - +
512A LEU 3.2 0.2 - - - -
513A GLN* 1.3 77.0 - - - +
515A ARG* 1.3 63.8 + - - +
517A TRP* 3.3 4.6 + - - +
518A PHE* 3.1 48.7 + - + -
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Residues in contact with ARG 515 (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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500A LYS* 3.5 42.7 - - + +
511A PRO 3.0 16.8 + - - +
512A LEU* 3.3 21.3 + - - +
514A VAL* 1.3 79.4 - - - +
516A VAL* 1.3 64.4 + - + +
518A PHE* 3.4 5.2 + - - +
519A ILE* 3.1 38.1 + - + +
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Residues in contact with VAL 516 (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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512A LEU* 2.9 32.0 + - + +
513A GLN* 4.2 3.6 - - - +
515A ARG* 1.3 73.9 - - + +
517A TRP* 1.3 60.9 + - - +
519A ILE* 3.2 13.4 + - + +
520A ASN* 2.8 49.7 + - - +
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Residues in contact with TRP 517 (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* 3.9 17.0 - - + -
482A ARG* 4.9 14.5 - - + +
485A LEU* 3.6 60.5 - - + +
486A GLU* 3.7 26.5 - - + -
489A PHE* 3.8 25.4 - + + -
513A GLN 2.9 19.0 + - - +
514A VAL* 3.5 4.3 - - - +
516A VAL* 1.3 77.7 - - - +
518A PHE* 1.3 83.4 + + - +
520A ASN* 3.7 6.5 - - + +
521A LYS* 2.8 52.4 + - + +
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Residues in contact with PHE 518 (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* 4.1 9.9 - - + -
488A VAL* 3.9 16.4 - - + -
489A PHE* 3.8 20.4 - + - -
492A LYS 3.5 22.4 - - - -
493A GLN 3.4 19.5 - - - -
494A SER* 4.5 0.9 - - - -
495A LEU* 3.4 36.3 - - + +
500A LYS* 5.7 2.2 - - + -
503A VAL* 5.2 0.7 - - + -
514A VAL* 3.1 34.9 + - + +
515A ARG* 3.7 9.0 - - - +
516A VAL 3.2 0.2 - - - -
517A TRP* 1.3 103.3 - + - +
519A ILE* 1.3 61.6 + - - +
521A LYS* 3.2 3.5 + - - +
522A ARG* 3.0 41.7 + - - +
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Residues in contact with ILE 519 (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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515A ARG* 3.1 36.9 + - + +
516A VAL* 3.2 17.0 + - + +
518A PHE* 1.3 75.3 - - - +
520A ASN* 1.3 65.1 + - - +
522A ARG* 3.1 25.5 + - - +
523A MET* 3.1 44.3 + - + +
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Residues in contact with ASN 520 (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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516A VAL* 2.8 45.3 + - - +
517A TRP* 3.7 6.9 - - + +
519A ILE* 1.3 76.7 - - - +
521A LYS* 1.3 61.0 + - - +
522A ARG 3.4 0.7 + - - -
523A MET* 3.5 23.9 + - - +
524A ARG* 4.9 1.2 + - - -
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Residues in contact with LYS 521 (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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486A GLU* 2.7 36.5 + - - -
489A PHE* 3.6 37.2 - - + -
517A TRP* 2.8 39.2 + - + +
518A PHE* 3.5 9.2 - - - +
520A ASN* 1.3 78.8 - - - +
522A ARG* 1.3 57.3 + - - +
523A MET 3.5 0.2 - - - -
524A ARG* 3.1 20.4 + - - -
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Residues in contact with ARG 522 (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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489A PHE* 4.0 15.3 - - + -
493A GLN* 2.7 48.1 + - + +
494A SER* 3.8 14.9 - - - +
495A LEU 4.9 1.0 - - - +
518A PHE* 3.0 35.0 + - - +
519A ILE* 3.1 30.0 + - - +
521A LYS* 1.3 75.0 - - - +
523A MET* 1.3 68.0 + - - +
524A ARG* 3.3 21.0 + - - +
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Residues in contact with MET 523 (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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519A ILE* 3.1 36.1 + - + +
520A ASN* 3.5 23.2 + - - +
522A ARG* 1.3 76.1 - - - +
524A ARG* 1.3 90.6 + - - +
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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