Contacts of the helix formed by residues 512 - 527 (chain D) in PDB entry 5MKF
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 VAL 512 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D ILE* 5.0 16.6 - - + -
502D TYR* 6.3 1.8 - - + -
508D ASN* 4.3 11.9 - - - +
509D CYS* 3.1 24.5 - - - +
511D ASP* 1.3 80.1 - - + +
513D VAL* 1.3 65.5 + - + +
515D VAL* 2.8 26.1 + - - +
516D VAL* 2.9 21.4 + - + +
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Residues in contact with VAL 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D CYS 4.1 13.2 - - - +
510D LEU* 3.1 25.2 + - + +
512D VAL* 1.3 80.2 - - + +
514D ILE* 1.3 64.5 + - - +
516D VAL* 2.8 23.5 + - + +
517D LEU* 2.9 37.8 + - + +
568D PHE* 5.2 18.8 - - + -
1006D PX6 5.4 10.3 - - + -
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Residues in contact with ILE 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D TYR* 5.3 11.0 - - + -
230D PHE* 5.1 10.5 - - + -
510D LEU 4.0 4.1 + - - +
511D ASP* 3.1 29.6 - - - +
513D VAL* 1.3 74.4 - - - +
515D VAL* 1.3 66.9 + - + +
517D LEU* 4.2 5.0 - - - +
518D SER* 3.0 30.5 + - - +
565D THR* 4.7 10.9 - - - +
568D PHE* 5.1 14.6 - - + +
569D VAL* 3.9 36.8 - - + -
572D LYS* 5.6 14.6 - - + -
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Residues in contact with VAL 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D ILE* 5.1 7.6 - - + -
487D TYR* 5.1 2.9 - - + +
488D VAL* 4.8 19.5 - - + +
491D GLU* 3.3 28.7 - - - +
511D ASP 4.3 4.0 - - - +
512D VAL* 2.8 15.4 + - - +
514D ILE* 1.3 82.2 - - + +
516D VAL* 1.3 68.2 + - - +
518D SER* 2.8 19.9 + - - +
519D VAL* 3.3 20.9 + - + +
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Residues in contact with VAL 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D VAL* 2.9 26.8 + - + +
513D VAL* 2.8 19.3 + - + +
515D VAL* 1.3 77.7 - - - +
517D LEU* 1.3 72.0 + - + +
519D VAL* 3.9 3.5 + - - +
520D VAL* 3.3 22.6 + - + +
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Residues in contact with LEU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D VAL* 2.9 34.3 + - + +
514D ILE* 4.3 1.6 - - - +
516D VAL* 1.3 83.3 - - + +
518D SER* 1.3 68.3 + - - +
520D VAL* 2.8 26.9 + - + +
521D ALA* 3.0 6.3 + - - +
561D ILE* 4.4 22.9 - - + +
564D VAL* 4.5 20.0 - - + -
565D THR* 3.6 28.7 - - + +
568D PHE* 4.8 5.6 - - + -
1006D PX6 5.0 19.3 - - + -
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Residues in contact with SER 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D PHE* 5.4 9.0 - - - -
484D ILE* 4.3 17.9 - - - +
514D ILE* 3.0 17.8 + - - -
515D VAL* 2.8 22.7 + - - -
517D LEU* 1.3 76.9 - - - +
519D VAL* 1.3 55.7 + - - +
521D ALA* 2.9 12.1 + - - +
522D ILE* 2.7 42.8 + - - +
565D THR* 4.2 11.4 - - - +
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Residues in contact with VAL 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484D ILE* 5.2 0.4 - - + -
488D VAL* 5.0 12.1 - - + -
515D VAL* 3.3 27.5 + - + +
516D VAL* 4.2 3.6 - - - +
517D LEU 3.2 0.8 - - - -
518D SER* 1.3 82.8 + - - +
520D VAL* 1.3 59.1 + - + +
522D ILE* 2.7 39.5 + - + +
523D GLY* 3.2 11.9 + - - +
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Residues in contact with VAL 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D VAL* 3.3 21.5 - - + +
517D LEU* 2.8 21.8 + - + +
519D VAL* 1.3 74.1 - - + +
521D ALA* 1.3 60.2 + - - +
523D GLY* 4.5 0.2 - - - -
524D ILE* 3.0 41.5 + - + +
561D ILE* 4.1 19.7 - - + -
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Residues in contact with ALA 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU 3.0 7.2 + - - +
518D SER* 2.9 14.6 + - - +
520D VAL* 1.3 77.1 - - - +
522D ILE* 1.3 67.9 + - + +
524D ILE* 3.2 24.3 - - - +
525D ASN* 3.1 14.2 + - - +
558D PHE* 3.8 20.7 - - + -
561D ILE* 4.8 16.7 - - + +
562D ALA* 5.1 3.8 - - - -
565D THR* 5.9 0.7 - - + -
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Residues in contact with ILE 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D PHE* 5.0 13.7 - - + -
481D CYS* 4.6 25.8 - - + +
484D ILE* 4.4 22.2 - - + -
488D VAL* 5.9 0.9 - - + -
518D SER* 2.7 21.9 + - - +
519D VAL* 2.7 40.0 + - + +
521D ALA* 1.3 68.9 - - + +
523D GLY* 1.3 62.0 + - - +
525D ASN* 2.6 34.9 - - - +
526D ILE* 4.7 4.6 - - + +
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Residues in contact with GLY 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D VAL* 3.2 8.6 + - - +
520D VAL 4.5 0.2 - - - -
522D ILE* 1.3 83.9 - - - +
524D ILE* 1.3 58.3 + - - +
525D ASN 2.8 1.7 + - - -
526D ILE* 5.6 0.2 - - - -
527D TYR* 2.4 50.6 + - - -
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Residues in contact with ILE 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D VAL* 3.0 35.4 - - + +
521D ALA* 3.2 19.7 - - - +
523D GLY* 1.3 73.6 - - - +
525D ASN* 1.3 61.9 + - - +
527D TYR* 5.6 0.7 - - + -
528D ARG* 3.0 50.6 - - + +
529D THR* 3.1 10.3 + - - +
554D TRP* 4.7 27.6 - - + -
557D GLN 5.4 0.4 - - - +
558D PHE* 4.0 27.8 - - + +
561D ILE* 4.8 4.5 - - + -
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Residues in contact with ASN 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ARG* 5.0 15.4 + - - +
477D GLU* 5.2 5.9 + - - -
521D ALA* 3.1 12.7 + - - +
522D ILE* 2.6 27.8 + - - +
523D GLY 2.8 1.8 + - - -
524D ILE* 1.3 81.3 - - - +
526D ILE* 1.3 98.0 + - - +
529D THR* 2.1 34.6 + - - +
530D SER* 3.1 4.7 + - - -
558D PHE* 4.3 24.3 - - + -
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Residues in contact with ILE 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ARG* 5.0 9.6 - - - +
477D GLU* 3.8 23.6 - - - +
478D ILE* 5.8 6.7 - - + -
481D CYS* 5.8 3.4 - - + -
522D ILE* 4.7 3.6 - - + +
523D GLY* 3.1 1.7 + - - +
525D ASN* 1.3 95.6 + - - +
527D TYR* 1.3 67.3 + - + +
530D SER* 2.2 54.3 + - - +
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Residues in contact with TYR 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D GLY* 2.4 42.7 + - - +
524D ILE* 5.6 0.4 - - + -
526D ILE* 1.3 76.3 - - - +
528D ARG* 1.3 93.0 + - + +
530D SER* 4.4 1.2 + - - -
531D ASN* 4.8 6.9 + - - +
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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