Contacts of the helix formed by residues 525 - 534 (chain A) in PDB entry 1MMG
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 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A LEU* 4.0 24.0 - - + -
516A LEU* 2.7 40.5 + - + +
517A ILE* 3.4 13.4 + - + +
524A GLY* 1.4 71.4 - - - +
526A LEU* 1.3 67.4 + - + +
528A LEU* 3.8 1.6 - - - +
529A LEU* 2.9 23.6 + - + +
547A LEU* 4.1 20.6 - - + +
551A PHE* 4.0 17.0 - - + -
558A TYR* 5.0 1.8 - - + -
568A PHE* 3.9 32.8 - - + -
570A VAL* 4.0 12.3 - - + -
584A TRP* 4.5 8.7 - - + -
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Residues in contact with LEU 526 (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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466A PHE* 4.0 20.4 - - + -
469A LEU* 4.2 17.5 - - + -
470A CYS* 5.6 4.3 - - - -
473A TYR* 4.1 21.3 - - + -
517A ILE* 2.9 37.4 + - + +
518A ASP* 4.4 8.3 - - + -
525A ILE* 1.3 82.8 - - + +
527A ALA* 1.3 55.9 + - - +
529A LEU* 3.3 9.1 + - + +
530A ASP* 2.8 34.0 + - - +
631A ALA* 4.0 36.1 - - + +
634A TYR* 6.0 2.0 - - + -
635A LYS* 4.8 8.5 - - + +
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Residues in contact with ALA 527 (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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517A ILE 4.5 0.8 + - - -
518A ASP 5.8 0.8 + - - -
519A GLY 3.5 24.1 + - - +
520A ARG* 5.0 8.1 - - + +
523A PRO* 3.7 16.4 - - + -
524A GLY 3.2 7.5 + - - +
526A LEU* 1.3 76.1 - - - +
528A LEU* 1.4 65.8 + - - +
530A ASP* 3.1 10.7 + - - +
531A GLU* 3.0 21.8 + - - +
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Residues in contact with LEU 528 (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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523A PRO* 4.0 17.0 - - + +
524A GLY 2.9 14.8 + - - +
525A ILE 3.9 3.1 - - - +
527A ALA* 1.4 78.1 - - - +
529A LEU* 1.3 62.4 + - - +
531A GLU* 3.2 17.0 + - - +
532A GLN* 3.0 28.7 + - - +
543A LEU* 4.6 1.6 - - + -
546A LYS* 4.3 20.8 - - + +
547A LEU* 3.9 15.0 - - + -
550A HIS* 3.7 42.8 - - + +
551A PHE* 3.5 37.7 - - + -
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Residues in contact with LEU 529 (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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466A PHE* 3.7 33.4 - - + -
525A ILE* 2.9 19.8 + - + +
526A LEU* 3.6 12.8 - - + +
528A LEU* 1.3 73.9 - - - +
530A ASP* 1.3 67.0 + - - +
532A GLN* 3.3 3.5 + - - +
533A SER* 2.8 29.7 + - - +
543A LEU* 3.9 37.1 - - + +
547A LEU* 6.5 0.2 - - + -
584A TRP* 3.9 24.9 - - + +
585A LEU* 4.3 3.8 - - + -
588A ASN* 3.7 32.3 - - + +
631A ALA* 4.5 2.7 - - + -
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Residues in contact with ASP 530 (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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526A LEU* 2.8 19.8 + - - +
527A ALA* 3.1 11.1 + - - +
529A LEU* 1.3 77.0 - - - +
531A GLU* 1.3 58.8 + - - +
533A SER* 2.9 21.7 + - - -
534A VAL* 3.7 8.8 + - - +
588A ASN* 2.8 17.5 + - - +
629A THR* 2.7 36.6 + - + +
631A ALA* 4.0 4.5 - - - +
632A ALA* 4.2 12.5 + - - +
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Residues in contact with GLU 531 (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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523A PRO* 5.9 1.0 - - - +
527A ALA 3.0 13.2 + - - +
528A LEU* 3.3 21.0 - - + +
530A ASP* 1.3 79.0 - - - +
532A GLN* 1.3 64.8 + - + +
533A SER 3.2 0.5 + - - -
534A VAL* 3.3 10.8 + - - +
535A PHE* 3.3 28.0 - - + -
546A LYS* 4.4 20.2 + - + +
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Residues in contact with GLN 532 (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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528A LEU 3.0 16.8 + - - +
529A LEU 3.6 2.5 - - - +
531A GLU* 1.3 82.0 - - + +
533A SER* 1.3 62.6 + - - +
534A VAL 3.2 0.9 + - - -
535A PHE* 3.5 21.7 + - - +
538A ALA* 2.9 26.0 - - - +
542A THR* 2.4 47.3 - - - +
543A LEU* 3.7 21.7 - - + +
546A LYS* 4.1 20.9 - - + +
585A LEU* 3.4 20.3 - - + +
589A LYS* 4.7 0.3 + - - -
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Residues in contact with SER 533 (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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529A LEU* 2.8 16.8 + - - +
530A ASP* 2.9 12.6 + - - -
532A GLN* 1.3 79.2 - - - +
534A VAL* 1.3 58.9 + - - +
535A PHE 3.4 0.2 - - - -
585A LEU* 4.1 9.9 + - - +
588A ASN* 2.9 30.7 + - - +
589A LYS* 2.9 44.4 - - - +
629A THR* 4.6 7.4 - - - -
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Residues in contact with VAL 534 (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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530A ASP 3.9 8.3 - - - +
531A GLU* 3.6 12.8 - - - +
532A GLN 3.2 1.2 + - - -
533A SER* 1.3 78.6 - - - +
535A PHE* 1.3 79.1 + - + +
536A PRO* 3.1 13.5 - - - +
589A LYS* 5.4 0.2 - - - -
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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
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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