Contacts of the helix formed by residues 499 - 510 (chain G) in PDB entry 4P0S
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 THR 499 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472G ARG* 5.6 1.6 + - - +
475G PHE* 4.1 10.2 - - - -
497G TYR 3.3 1.6 + - - +
498G SER* 1.3 82.6 - - - +
500G PRO* 1.3 79.5 - - - +
501G ALA 3.9 2.9 + - - +
502G SER* 2.8 39.0 + - - +
503G LEU 3.3 5.0 + - - -
556H GLN 5.2 0.3 + - - -
558H THR 5.2 0.2 - - - -
559H THR 2.8 21.9 + - - -
560H LEU* 3.5 37.9 - - + +
561H GLN 5.8 0.2 - - - -
562H PRO* 5.8 3.1 - - - +
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Residues in contact with PRO 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472G ARG* 5.9 1.8 - - - +
475G PHE* 3.8 40.4 - - + -
478G GLN* 4.1 9.9 - - - +
499G THR* 1.3 90.4 - - - +
501G ALA* 1.3 60.8 + - - +
502G SER 3.3 0.3 + - - -
503G LEU* 3.5 4.2 + - - +
504G LEU* 3.3 28.0 + - + +
544G TYR* 5.8 4.8 - - + -
556H GLN* 3.8 24.0 - - - +
557H MET* 3.9 31.4 - - + +
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Residues in contact with ALA 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499G THR* 3.1 3.1 + - + +
500G PRO* 1.3 79.9 - - - +
502G SER* 1.3 57.6 + - - +
504G LEU* 3.5 14.5 + - + +
505G ALA* 3.0 27.4 + - - +
557H MET 4.2 6.8 + - - +
558H THR* 3.7 24.9 - - - +
560H LEU* 3.9 17.3 - - + -
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Residues in contact with SER 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G ARG 4.8 0.7 + - - -
497G TYR* 3.6 27.3 - - - -
498G SER* 3.9 7.3 + - - -
499G THR* 2.8 34.0 + - - +
501G ALA* 1.3 76.7 - - - +
503G LEU* 1.3 64.4 + - - -
504G LEU 3.2 0.2 - - - -
505G ALA* 3.3 14.6 + - - +
506G ALA* 3.4 9.0 + - - +
560H LEU* 4.9 5.8 - - - -
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Residues in contact with LEU 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475G PHE* 4.4 16.8 - - + -
479G LEU* 5.6 1.6 - - + -
497G TYR* 3.8 33.2 - - + +
499G THR 3.3 3.6 + - - -
500G PRO 3.5 7.2 + - - +
502G SER* 1.3 77.2 - - - +
504G LEU* 1.3 58.4 + - + +
506G ALA* 3.4 2.1 + - - +
507G TYR* 3.0 60.4 + - + -
519G LEU* 5.3 1.3 - - + -
520G LEU* 3.7 26.0 - - + -
540G LEU* 5.6 2.0 - - + -
544G TYR* 3.6 35.4 - - + -
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Residues in contact with LEU 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500G PRO* 3.3 18.5 + - + +
501G ALA* 3.5 14.8 - - + +
502G SER 3.2 0.4 - - - -
503G LEU* 1.3 78.8 - - + +
505G ALA* 1.3 59.4 + - - +
507G TYR* 4.1 5.1 - - + +
508G ASP* 3.0 33.9 + - + +
544G TYR* 3.9 25.1 - - + +
507H PRO* 6.1 2.5 - - + -
508H GLN* 3.7 28.3 - - - +
511H VAL* 4.1 31.0 - - + -
557H MET* 5.4 6.7 - - + +
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Residues in contact with ALA 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501G ALA 3.0 16.8 + - - +
502G SER* 3.3 8.0 + - - +
504G LEU* 1.3 75.7 - - - +
506G ALA* 1.3 58.8 + - - +
508G ASP* 4.0 4.8 - - - +
509G ALA* 2.8 32.9 + - - +
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Residues in contact with ALA 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497G TYR* 3.6 28.0 - - + +
502G SER 3.4 4.9 + - - +
503G LEU 3.9 4.9 - - - +
505G ALA* 1.3 77.9 - - - +
507G TYR* 1.3 66.4 + - - +
509G ALA* 3.3 6.8 + - - +
510G CYS* 2.9 26.2 + - - -
519G LEU* 3.6 21.0 - - + +
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Residues in contact with TYR 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503G LEU* 3.0 47.3 + - + +
504G LEU* 4.1 6.3 - - + +
506G ALA* 1.3 77.3 - - - +
508G ASP* 1.3 55.7 + - - +
510G CYS* 3.3 17.1 - - - +
516G GLN* 2.7 66.2 + - + +
519G LEU* 3.8 18.4 - - + -
520G LEU* 3.0 27.1 - - + +
537G SER 3.8 3.3 + - - -
540G LEU* 3.7 15.0 - - - +
541G SER* 3.5 23.0 + - - -
544G TYR* 4.2 9.4 - - + +
545G CYS* 3.8 20.4 - - - -
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Residues in contact with ASP 508 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504G LEU* 3.0 20.2 + - + +
505G ALA* 4.0 5.3 - - - +
507G TYR* 1.3 73.5 - - - +
509G ALA* 1.3 60.0 + - - +
510G CYS 3.0 13.8 + - - +
516G GLN* 4.6 3.1 - - - +
547G TYR* 5.0 7.7 + - - -
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Residues in contact with ALA 509 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505G ALA 2.8 20.8 + - - +
506G ALA* 3.3 8.7 + - - +
508G ASP* 1.3 72.4 - - - +
510G CYS* 1.3 66.7 + - - +
511G ALA* 5.2 0.7 - - - +
515G GLU* 4.6 0.5 - - - +
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Residues in contact with CYS 510 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506G ALA 2.9 25.6 + - - -
507G TYR* 3.3 20.2 - - - +
508G ASP 3.0 10.7 - - - +
509G ALA* 1.3 85.8 - - - +
511G ALA* 1.3 61.3 + - - +
512G THR 4.2 1.6 - - - +
515G GLU* 3.1 47.3 - - + +
516G GLN* 3.9 12.5 + - + +
519G LEU* 4.0 13.0 - - - -
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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