Contacts of the helix formed by residues 499 - 505 (chain G) in PDB entry 4D1Q
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 499 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ARG* 3.4 0.9 - - - -
536B GLU* 3.6 30.1 + - - -
498G ILE* 1.3 76.0 - - - +
500G THR* 1.3 68.3 + - - +
501G THR* 2.8 13.6 + - - -
502G SER* 2.5 26.7 + - - -
503G PHE* 2.9 19.4 + - - +
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Residues in contact with THR 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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369B ARG* 3.0 15.6 + - - +
373B GLU* 3.2 25.9 + - - +
384B PHE* 3.3 33.7 - - + -
499G SER* 1.3 71.8 - - - +
501G THR* 1.3 59.2 + - + +
503G PHE* 3.4 2.7 - - - +
504G PHE* 3.0 46.0 + - + -
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Residues in contact with THR 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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384B PHE* 6.1 2.0 - - + -
436B TYR* 3.9 11.9 - - - +
534B LEU* 3.7 33.4 - - + +
535B SER 4.1 6.5 - - - +
536B GLU* 3.4 30.4 + - - +
538B PHE 4.9 7.2 - - - +
499G SER* 2.8 10.4 + - - -
500G THR* 1.3 78.3 - - + +
502G SER* 1.3 65.7 + - - -
504G PHE 3.4 0.3 + - - -
505G PHE* 2.9 42.6 + - - +
509G THR* 4.2 3.5 + - - -
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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
----------------------------------------------------------
391B LYS* 5.0 0.7 + - - -
536B GLU* 4.7 3.3 + - - +
498G ILE* 3.6 14.6 - - - -
499G SER* 2.5 32.5 + - - -
501G THR* 1.3 76.4 + - - +
503G PHE* 1.3 65.2 + - - +
505G PHE 3.9 0.9 - - - -
506G PRO* 3.3 26.1 - - - +
509G THR* 3.8 27.6 + - - +
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Residues in contact with PHE 503 (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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366B GLY* 3.8 17.5 - - - -
369B ARG* 3.5 45.1 - - + +
370B ILE* 3.9 18.6 - - + -
391B LYS* 3.0 60.7 + - + +
395B ILE* 5.7 0.2 - - + -
495G SER* 4.4 17.5 - - - -
498G ILE* 3.4 16.8 - - + +
499G SER 2.9 10.7 + - - +
500G THR* 3.4 11.9 - - - +
501G THR 3.1 0.2 - - - -
502G SER* 1.3 81.5 - - - +
504G PHE* 1.3 89.0 + + - +
506G PRO* 4.0 1.9 - - - +
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Residues in contact with PHE 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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370B ILE* 5.1 1.3 - - - -
373B GLU* 3.8 26.5 - - + -
384B PHE* 3.5 34.5 - + + -
387B PRO* 3.5 37.6 - - + +
388B SER* 2.9 31.9 - - - -
390B LEU* 5.7 2.1 - - - +
391B LYS* 5.0 6.5 + - + +
394B GLU* 5.6 0.5 - - - +
500G THR* 3.0 34.5 + - + +
503G PHE* 1.3 101.5 - + - +
505G PHE* 1.3 87.5 + + + +
506G PRO* 3.8 5.1 - - - +
507G GLN* 4.3 1.6 + - - +
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Residues in contact with PHE 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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384B PHE* 5.2 7.0 - + - -
387B PRO* 3.9 18.6 - - + -
433B PHE* 3.7 34.3 - + - -
436B TYR* 3.4 35.4 - + - -
438B PRO* 5.8 3.4 - - + -
441B HIS* 4.2 17.5 - + - -
534B LEU* 3.8 24.7 - - + -
501G THR* 2.9 27.3 + - - +
502G SER 3.6 0.8 - - - +
504G PHE* 1.3 99.2 - + + +
506G PRO* 1.3 67.1 - - - +
507G GLN* 3.0 11.4 - - - +
508G LEU* 4.2 13.7 - - + -
509G THR* 3.3 16.1 + - - -
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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