Contacts of the helix formed by residues 521 - 536 (chain A) in PDB entry 1MD9
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 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 3.5 19.4 + - - -
513A PRO 2.9 17.6 + - - -
514A GLN 4.4 2.9 - - - -
515A THR* 4.1 19.8 - - - +
520A VAL* 1.3 75.7 - - - +
522A LYS* 1.3 64.1 + - - +
523A LYS* 3.0 1.1 - - - +
524A ALA* 2.8 36.6 + - - +
525A LEU* 3.0 12.6 + - - +
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Residues in contact with LYS 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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431A ASP* 3.7 40.3 - - + +
442A ALA* 3.7 11.5 - - - +
443A GLU* 4.7 2.2 - - - +
446A GLU* 2.4 33.1 + - - -
459A ALA* 4.0 16.2 - - + -
460A MSE 3.3 22.4 + - - +
461A VAL* 3.9 14.5 - - + +
520A VAL* 3.6 9.5 + - + +
521A SER* 1.3 72.6 - - - +
523A LYS* 1.3 63.9 + - - +
525A LEU* 3.2 9.0 + - + +
526A ARG* 2.7 32.2 + - - +
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Residues in contact with LYS 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.2 40.2 + - - +
194A THR* 4.3 9.3 - - - +
195A GLY* 4.0 21.8 - - - +
521A SER* 3.0 1.7 + - - +
522A LYS* 1.3 76.7 - - - +
524A ALA* 1.3 66.3 + - - +
526A ARG* 2.8 40.0 + - + +
527A GLU* 3.0 36.2 + - + +
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Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PRO* 3.6 22.7 - - + -
521A SER* 2.8 29.7 + - - +
523A LYS* 1.3 80.7 - - - +
525A LEU* 1.3 61.9 + - - +
527A GLU* 2.9 28.6 + - - +
528A ALA* 2.9 12.5 + - - +
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Residues in contact with LEU 525 (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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459A ALA* 3.5 35.2 - - + +
461A VAL* 3.6 24.0 - - + -
475A PHE* 3.6 41.6 - - + -
509A VAL* 6.1 0.4 - - + -
512A PHE* 4.6 5.4 - - + -
513A PRO* 3.3 30.3 - - + -
520A VAL* 3.7 16.4 - - + -
521A SER 3.0 11.3 + - - +
522A LYS* 3.6 4.9 - - - +
524A ALA* 1.3 74.7 - - - +
526A ARG* 1.3 66.7 + - - +
528A ALA* 3.2 7.4 + - + +
529A ILE* 3.1 19.4 + - - +
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 3.4 22.5 + - - +
431A ASP* 3.3 29.9 + - - +
461A VAL* 3.1 33.0 - - + +
462A SER* 3.8 22.3 + - - +
522A LYS* 2.7 19.3 + - - +
523A LYS* 2.8 45.5 + - + +
525A LEU* 1.3 74.2 - - - +
527A GLU* 1.3 63.9 + - + +
529A ILE* 3.3 5.0 - - - +
530A SER* 3.0 21.5 + - - -
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS* 3.0 42.9 + - + +
524A ALA* 2.9 14.7 + - - +
526A ARG* 1.3 75.0 - - + +
528A ALA* 1.3 68.7 + - - +
530A SER* 3.0 8.9 + - - -
531A GLU* 2.9 35.6 + - + +
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Residues in contact with ALA 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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475A PHE* 4.1 13.9 - - + -
524A ALA 2.9 10.9 + - - +
525A LEU* 3.2 17.5 - - + +
527A GLU* 1.3 81.1 - - - +
529A ILE* 1.3 59.7 + - - +
531A GLU* 2.8 24.3 + - - +
532A LYS* 3.1 19.6 + - + +
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Residues in contact with ILE 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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461A VAL* 4.5 4.7 - - + -
462A SER 4.1 10.3 - - - +
463A MSE 3.9 29.8 - - + -
464A PRO* 5.3 0.2 - - + -
473A CYS* 3.6 24.9 - - + -
475A PHE* 4.0 12.9 - - + -
505A ARG* 3.5 44.0 - - - +
507A GLU* 4.0 6.3 - - + -
525A LEU 3.1 7.4 + - - +
526A ARG* 3.3 12.1 - - - +
528A ALA* 1.3 79.3 - - - +
530A SER* 1.3 61.3 + - - +
532A LYS* 3.4 9.1 + - + -
533A LEU* 2.9 34.5 + - + +
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Residues in contact with SER 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PRO* 4.5 18.7 - - - +
526A ARG 3.0 12.3 + - - -
527A GLU* 3.0 13.9 + - - -
528A ALA 2.9 0.2 + - - -
529A ILE* 1.3 79.3 - - - +
531A GLU* 1.3 58.6 + - - +
533A LEU* 3.5 11.5 + - - +
534A LEU* 3.0 39.1 + - - +
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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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527A GLU* 2.9 33.2 + - - +
528A ALA* 2.8 10.6 + - - +
530A SER* 1.3 77.0 - - - +
532A LYS* 1.3 55.8 + - + +
534A LEU* 3.0 14.3 + - + +
535A ALA* 2.7 35.3 + - - +
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Residues in contact with LYS 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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475A PHE* 6.1 3.8 - - + -
505A ARG* 3.9 20.9 - - - +
507A GLU* 3.4 27.1 + - + +
508A PHE 5.9 1.0 + - - -
509A VAL* 6.2 1.6 - - - +
528A ALA* 3.1 18.3 + - - +
529A ILE* 3.7 13.2 - - + +
531A GLU* 1.3 76.6 - - + +
533A LEU* 1.3 65.6 + - - +
535A ALA* 2.8 26.6 + - - +
536A GLY 3.6 1.9 + - - -
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A MSE 3.8 28.3 - - + -
464A PRO* 3.7 39.3 - - + +
505A ARG* 3.5 27.4 - - - +
529A ILE* 2.9 26.7 + - + +
530A SER* 3.6 5.4 - - - +
532A LYS* 1.3 75.6 - - - +
534A LEU* 1.3 61.6 + - + +
536A GLY* 3.2 15.8 + - - -
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Residues in contact with LEU 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 SER* 3.0 35.7 + - - +
531A GLU* 3.0 15.3 + - + +
533A LEU* 1.3 71.6 - - + +
535A ALA* 1.3 55.1 + - - +
536A GLY 2.7 26.1 + - - +
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Residues in contact with ALA 535 (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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531A GLU 2.7 16.2 + - - +
532A LYS* 2.8 19.7 + - - +
534A LEU* 1.3 72.0 - - - +
536A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 536 (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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532A LYS 3.6 1.8 + - - -
533A LEU 3.2 14.5 + - - -
534A LEU 2.7 13.6 + - - +
535A ALA* 1.3 80.8 - - - +
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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