Contacts of the strand formed by residues 467 - 475 (chain M) in PDB entry 5D4E
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 467 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M ILE* 5.4 0.2 - - + -
328M LEU* 4.7 14.1 + - + +
331M ARG 5.4 3.0 + - - +
333M ILE* 3.6 37.0 - - + -
410M ILE* 4.1 7.6 - - + -
437M ARG* 3.0 49.1 + - + -
438M ILE* 3.9 30.7 - - + -
455M LEU* 3.9 10.5 - - + -
459M ALA* 3.8 21.5 - - + -
460M ARG 3.3 7.2 - - - +
461M VAL* 4.3 6.1 - - + +
466M PHE* 1.3 73.6 - - - +
468M ARG* 1.3 63.5 + - - +
487M THR* 4.1 5.9 - - - -
488M ALA 4.7 0.3 + - - -
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Residues in contact with ARG 468 (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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437M ARG* 4.6 2.2 - - - -
459M ALA* 3.4 5.2 - - - +
460M ARG* 2.5 40.2 + - + +
462M ASP* 3.0 48.6 + - - +
466M PHE 3.9 2.0 - - - +
467M ILE* 1.3 78.4 - - - +
469M THR* 1.3 60.3 + - - +
485M TYR* 3.1 49.6 + - + +
486M MET* 3.2 15.8 - - - +
487M THR* 3.6 22.0 - - + +
490M GLU* 5.6 5.3 - - - +
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Residues in contact with THR 469 (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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435M TYR 4.1 2.9 - - - +
436M GLY* 3.3 26.4 + - - -
437M ARG* 3.4 36.1 - - - +
468M ARG* 1.3 73.6 - - - +
470M PRO* 1.3 65.6 + - - +
471M TYR* 3.5 25.9 - - + +
485M TYR* 3.7 3.8 - - - -
486M MET 3.1 21.8 + - - +
538M GLN* 2.9 27.2 + - - -
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Residues in contact with PRO 470 (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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13M ILE* 3.9 3.6 - - + -
458M TYR* 3.6 29.2 - - + +
469M THR* 1.3 91.7 + - - +
471M TYR* 1.3 68.7 + - - +
483M VAL* 3.6 12.3 - - + -
484M VAL 3.6 6.1 - - - +
485M TYR* 3.4 35.9 - - + +
534M VAL* 3.4 20.2 - - + +
538M GLN* 3.0 31.3 + - + +
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Residues in contact with TYR 471 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M TYR* 4.0 7.6 - + - -
469M THR* 3.5 36.9 - - + +
470M PRO* 1.3 76.9 - - - +
472M ARG* 1.3 64.6 + - - +
483M VAL* 3.2 5.4 - - - -
484M VAL* 2.9 30.9 + - - +
486M MET* 3.6 35.9 - - + -
491M GLU* 2.9 28.6 + - + -
496M ILE* 3.5 41.7 - - + -
516M ARG* 3.0 16.8 + - - -
531M PHE* 4.1 7.6 - - + -
532M MET 3.6 9.6 - - - +
533M ASP* 3.6 16.2 - - - -
534M VAL* 4.0 3.1 - - - -
538M GLN* 4.4 4.0 - - - -
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Residues in contact with ARG 472 (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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10M ARG* 4.2 17.3 + - - +
12M VAL* 3.3 40.5 - - + +
471M TYR* 1.3 75.8 - - - +
473M ARG* 1.3 65.0 + - - +
474M VAL* 3.4 1.0 + - - +
479M VAL* 3.4 32.0 + - + +
480M THR 3.7 18.8 + - - +
481M ASP* 4.3 1.4 + - - +
482M GLU 3.4 3.1 - - - +
483M VAL* 4.3 13.9 - - + -
499M ALA* 5.3 1.2 + - - +
503M LEU* 4.0 12.1 - - - +
506M ASN* 5.5 1.0 + - - -
531M PHE* 3.2 8.1 - - - -
532M MET* 2.9 61.3 + - - +
533M ASP 4.0 11.9 + - - -
534M VAL* 4.5 15.9 + - + +
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Residues in contact with ARG 473 (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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471M TYR 4.1 0.4 + - - -
472M ARG* 1.3 71.3 - - - +
474M VAL* 1.3 62.3 + - - +
475M VAL* 3.8 24.7 - - + -
479M VAL* 3.8 0.3 - - - -
480M THR* 2.9 43.1 + - + +
482M GLU* 2.9 55.5 + - - +
484M VAL* 3.8 11.1 - - + +
494M TYR* 5.6 4.2 + - - -
530M GLU 4.6 2.9 - - - -
531M PHE* 3.4 38.2 - - + -
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Residues in contact with VAL 474 (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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472M ARG 3.6 10.8 - - - +
473M ARG* 1.3 78.8 - - - +
475M VAL* 1.3 64.2 + - - +
476M GLY 4.1 0.5 + - - -
477M GLY* 4.3 9.6 - - - +
478M VAL 3.3 22.0 - - - +
479M VAL* 3.9 18.6 - - + -
508M ILE* 4.5 2.7 - - + -
529M VAL* 3.1 44.1 - - + +
530M GLU* 2.8 20.4 + - - +
531M PHE 3.7 16.4 - - - -
532M MET* 3.7 14.1 - - + -
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Residues in contact with VAL 475 (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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473M ARG* 3.8 24.8 + - + -
474M VAL* 1.3 75.3 - - - +
476M GLY* 1.3 68.8 + - - +
477M GLY 3.4 1.1 - - - -
478M VAL* 2.9 28.9 + - + +
480M THR* 5.2 8.3 - - + -
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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