Contacts of the helix formed by residues 513 - 522 (chain M) in PDB entry 6D6R
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 513 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510M ARG* 5.1 13.7 - - - +
511M TRP 3.6 3.4 + - - -
512M ILE* 1.3 77.7 - - - +
514M SER* 1.3 67.9 + - - +
515M GLY* 3.6 7.6 + - - -
516M GLU* 2.9 31.2 + - - +
517M TYR* 2.9 12.3 + - - +
557M ASP* 3.9 19.8 + - - +
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Residues in contact with SER 514 (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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512M ILE 3.9 2.2 + - - -
513M SER* 1.3 73.2 + - - +
515M GLY* 1.3 63.5 + - - +
517M TYR* 3.6 8.7 - - - +
518M ILE* 2.9 33.6 + - - +
550M GLN* 3.9 14.6 + - - -
551M LEU* 3.3 21.9 + - - +
554M GLY 3.1 22.9 + - - -
555M SER 3.6 16.0 + - - -
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Residues in contact with GLY 515 (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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513M SER* 3.0 7.5 + - - -
514M SER* 1.3 79.0 - - - +
516M GLU* 1.3 55.5 + - - +
518M ILE* 3.8 3.5 - - - +
519M GLN* 2.9 28.3 + - - +
556M ALA* 4.6 9.2 - - - +
557M ASP* 4.3 27.7 - - - +
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Residues in contact with GLU 516 (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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394M PHE* 5.0 0.2 - - - -
483M GLU* 5.7 0.9 - - - -
503M LYS* 2.5 40.8 + - - +
505M ASP* 4.6 1.0 - - - +
510M ARG* 2.9 26.7 + - - -
512M ILE* 3.5 12.2 - - + +
513M SER* 2.9 20.5 + - - +
515M GLY* 1.3 71.6 - - - +
517M TYR* 1.3 67.4 + - - +
519M GLN* 3.6 7.7 - - + +
520M MET* 2.9 38.0 + - + +
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Residues in contact with TYR 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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318M HIS* 2.9 37.7 + + - +
498M PHE* 3.3 43.4 - + - -
512M ILE* 4.4 15.0 - - + +
513M SER 2.9 12.1 + - - +
514M SER* 3.6 11.4 - - - +
516M GLU* 1.3 77.3 - - - +
518M ILE* 1.3 66.6 + - + +
520M MET* 3.4 2.3 + - - +
521M SER* 2.8 41.1 + - - -
535M VAL* 3.5 5.7 - - - +
537M LEU* 4.7 14.8 - - + +
551M LEU* 3.9 35.2 - - + -
552M LEU* 4.2 27.3 - - + +
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Residues in contact with ILE 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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162M HIS* 4.0 33.0 - - + +
285M THR* 5.0 5.8 - - - +
312M ARG* 4.2 8.1 - - - +
514M SER* 2.9 35.7 + - - +
515M GLY* 3.9 3.6 - - - +
517M TYR* 1.3 81.9 - - + +
519M GLN* 1.3 67.9 + - - +
520M MET 3.0 1.6 - - - -
521M SER* 4.2 7.2 - - - -
522M GLY* 2.9 22.9 + - - -
552M LEU 5.0 6.5 - - - +
554M GLY 4.0 11.7 - - - +
555M SER* 4.9 0.7 - - - -
556M ALA* 4.7 14.8 - - + +
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Residues in contact with GLN 519 (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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163M THR* 4.3 15.1 + - - -
255M HIS* 3.7 24.8 + - + -
284M ALA* 4.1 16.5 - - - +
486M ALA* 2.9 41.4 + - + +
487M MET* 4.1 23.7 + - + +
515M GLY 2.9 18.1 + - - +
516M GLU* 3.2 9.6 + - - +
518M ILE* 1.3 77.2 - - - +
520M MET* 1.3 60.8 + - + +
522M GLY* 4.1 4.3 + - - -
523M ARG* 4.5 10.4 + - - +
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Residues in contact with MET 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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392M PHE* 3.9 26.2 - - + -
394M PHE* 3.5 31.4 - - + -
482M THR 3.7 6.3 - - - +
483M GLU* 3.6 21.5 - - + -
486M ALA* 3.6 24.5 - - + -
496M VAL* 4.9 2.5 - - - +
498M PHE* 3.5 35.2 - - + -
503M LYS* 5.5 0.2 - - - +
516M GLU* 2.9 28.2 + - + +
517M TYR* 5.4 0.2 - - - -
519M GLN* 1.3 76.1 - - + +
521M SER* 1.3 65.3 + - - +
522M GLY 3.1 2.2 - - - -
523M ARG* 2.9 30.0 + - - +
524M ALA 4.3 0.2 + - - -
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Residues in contact with SER 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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312M ARG* 5.4 1.3 - - - -
316M LEU* 3.6 31.2 - - - +
318M HIS* 4.0 6.5 - - - -
496M VAL* 4.6 9.9 - - - -
498M PHE* 4.1 7.0 - - - -
517M TYR* 2.8 46.1 + - - -
518M ILE* 3.2 9.4 + - - -
520M MET* 1.3 75.3 - - - +
522M GLY* 1.3 62.5 + - - +
523M ARG 2.9 1.6 + - - -
524M ALA* 3.0 14.9 + - - +
535M VAL* 4.1 5.2 - - - +
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Residues in contact with GLY 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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162M HIS* 6.3 0.7 - - - -
163M THR* 4.8 12.7 - - - +
164M SER* 4.2 19.3 + - - -
312M ARG* 4.8 16.9 - - - +
316M LEU* 5.2 0.2 - - - -
492M PRO* 5.0 1.4 - - - +
518M ILE 2.9 16.9 + - - -
519M GLN 4.5 2.9 - - - -
520M MET 3.1 0.8 - - - -
521M SER* 1.3 75.0 - - - +
523M ARG* 1.3 71.5 + - - +
524M ALA 3.4 7.2 - - - +
525M GLY 5.3 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