Contacts of the helix formed by residues 516 - 528 (chain M) in PDB entry 2W4G
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 GLY 516 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489M GLN* 3.2 34.7 + - - -
492M ASN* 3.7 12.4 + - - +
493M HIS* 4.9 0.4 - - - -
514M ASP* 2.5 21.4 + - - -
515M PHE* 1.3 69.5 - - - +
517M MET* 1.3 49.0 + - - +
518M ASP 2.5 18.3 + - - -
519M LEU* 2.5 24.6 + - - +
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Residues in contact with MET 517 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489M GLN* 4.1 5.3 - - - +
513M ILE* 5.0 21.1 - - + -
514M ASP* 3.8 25.5 + - + +
516M GLY* 1.3 73.6 - - - +
518M ASP* 1.3 64.8 + - - +
519M LEU 3.0 0.9 + - - -
520M ALA* 3.2 17.9 + - + +
521M ALA 4.5 1.2 + - - -
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Residues in contact with ASP 518 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492M ASN* 5.6 0.2 - - - +
513M ILE* 5.8 3.3 - - - +
514M ASP 5.3 1.0 - - - +
515M PHE* 3.6 15.6 + - - +
516M GLY 2.5 6.5 + - - -
517M MET* 1.3 78.4 - - - +
519M LEU* 1.3 68.2 + - + +
520M ALA 3.8 0.2 + - - -
521M ALA* 4.4 9.9 + - - +
702M GLU* 5.9 1.1 - - - +
709M LYS* 5.6 3.8 + - - -
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Residues in contact with LEU 519 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485M GLU* 3.7 28.9 - - + +
488M GLN* 4.1 5.4 - - + -
489M GLN* 3.9 20.4 - - - +
492M ASN* 3.8 22.2 - - - +
515M PHE 3.9 0.2 - - - +
516M GLY* 2.5 25.6 + - - +
518M ASP* 1.3 84.3 - - + +
520M ALA* 1.3 64.3 + - - +
521M ALA 2.9 4.9 + - - -
522M CYS* 2.9 15.6 + - - +
523M ILE* 3.2 18.0 + - + +
584M TYR* 3.9 34.8 - - + -
702M GLU* 4.8 4.7 - - - +
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Residues in contact with ALA 520 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489M GLN* 3.4 19.8 - - - +
517M MET* 3.2 17.7 + - + +
519M LEU* 1.3 76.5 - - - +
521M ALA* 1.3 63.3 + - - +
523M ILE* 3.9 5.8 - - - +
524M GLU* 2.9 43.8 + - - +
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Residues in contact with ALA 521 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517M MET 4.5 1.2 + - - -
518M ASP 4.4 8.7 + - - +
519M LEU 2.9 1.0 + - - +
520M ALA* 1.3 79.7 - - - +
522M CYS* 1.3 66.0 + - - +
524M GLU* 3.4 10.8 + - - +
525M LEU* 3.4 12.6 + - - +
564M ASN* 3.2 24.0 - - - +
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Residues in contact with CYS 522 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485M GLU* 4.1 26.5 - - - +
519M LEU* 2.9 8.9 + - - +
521M ALA* 1.3 79.3 - - - +
523M ILE* 1.3 65.9 + - - +
525M LEU* 3.2 20.6 + - - +
526M ILE* 3.4 13.4 + - - +
564M ASN* 4.0 9.1 + - - +
581M LEU* 4.2 25.4 - - - -
582M VAL 3.9 26.2 - - - +
583M HIS* 4.3 4.5 - - - -
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Residues in contact with ILE 523 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482M PHE* 4.2 14.4 - - + -
485M GLU* 4.0 28.9 - - + +
486M LYS* 4.4 23.1 - - + -
489M GLN* 3.7 30.1 - - - +
519M LEU* 3.2 19.2 + - + +
520M ALA* 3.9 5.6 - - - +
522M CYS* 1.3 76.5 - - - +
524M GLU* 1.3 70.9 + - - +
526M ILE* 2.9 14.7 + - - +
527M GLU* 3.0 39.8 + - + +
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Residues in contact with GLU 524 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520M ALA* 2.9 46.9 + - - +
521M ALA* 4.2 4.9 - - - +
523M ILE* 1.3 78.8 - - - +
525M LEU* 1.3 58.8 + - - +
527M GLU* 4.7 3.3 - - - +
528M LYS* 2.8 74.4 + - + +
531M GLY* 4.7 0.3 - - - -
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Residues in contact with LEU 525 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521M ALA 3.4 9.8 + - - +
522M CYS* 3.2 11.8 + - - +
523M ILE 3.1 0.2 - - - -
524M GLU* 1.3 77.2 - - - +
526M ILE* 1.3 58.0 + - - +
531M GLY* 3.1 24.4 - - - -
532M ILE* 3.1 14.1 + - + +
558M HIS* 3.7 31.9 - - + +
562M SER* 3.8 22.7 - - - +
564M ASN* 3.9 34.1 - - + +
565M PHE* 4.2 10.5 - - + +
581M LEU* 4.3 23.3 - - + -
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Residues in contact with ILE 526 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478M LEU* 4.2 17.0 - - + -
482M PHE* 3.7 33.4 - - + -
485M GLU* 6.3 0.7 - - + -
522M CYS* 3.5 21.3 - - - +
523M ILE* 2.9 7.5 + - - +
525M LEU* 1.3 81.9 - - + +
527M GLU* 1.3 60.7 + - - +
528M LYS 3.6 1.0 + - - +
531M GLY 3.9 2.1 - - - -
532M ILE* 3.8 13.2 + - + -
533M PHE* 3.4 56.6 + - + +
581M LEU* 4.0 28.7 - - + -
583M HIS* 4.6 6.5 - - + -
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Residues in contact with GLU 527 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482M PHE* 3.5 20.0 - - + -
486M LYS* 3.3 29.0 + - - -
523M ILE* 3.0 31.1 + - + +
524M GLU* 4.7 5.0 - - - +
526M ILE* 1.3 75.2 - - - +
528M LYS* 1.3 73.3 + - + +
529M PRO* 3.9 0.7 - - - +
533M PHE* 5.1 0.2 - - - -
654M ARG* 3.9 27.3 + - + +
658M ASN* 4.7 9.9 + - - +
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Residues in contact with LYS 528 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524M GLU* 2.8 64.9 + - + +
526M ILE 4.0 1.2 - - - +
527M GLU* 1.3 81.9 - - + +
529M PRO* 1.3 75.2 - - + +
530M MET 3.5 2.9 - - - +
531M GLY* 3.0 23.0 + - - +
534M SER* 4.4 3.3 + - - -
654M ARG* 5.2 1.1 + - - -
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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