Contacts of the helix formed by residues 539 - 547 (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 LYS 539 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B PRO* 5.2 4.1 - - - +
537G ASP* 3.1 21.9 + - - +
538G PHE* 1.3 80.9 - - - +
540G VAL* 1.3 65.7 + - - +
541G MET* 2.8 7.1 + - + +
542G GLU* 2.9 48.5 + - + +
543G TRP* 3.4 8.8 + - - +
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Residues in contact with VAL 540 (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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380G PRO* 3.5 22.4 - - + +
383G CYS* 5.0 0.2 - - - -
435G PHE 3.5 12.1 - - - +
436G TYR* 3.7 29.7 - - + -
437G PRO* 3.5 32.3 - - + -
538G PHE* 3.5 16.9 + - + -
539G LYS* 1.3 70.9 - - - +
541G MET* 1.3 64.9 + - - +
543G TRP* 4.2 0.8 - - - +
544G TRP* 3.4 26.0 + - + +
562G LEU* 3.2 26.9 - - + +
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Residues in contact with MET 541 (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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199G HIS* 3.3 34.1 - - + +
202G ASN* 3.8 17.9 - - - +
204G LEU* 3.6 46.4 - - + +
379G SER* 5.5 0.4 - - - -
380G PRO* 3.5 30.7 - - + +
539G LYS* 2.8 9.7 + - + -
540G VAL* 1.3 78.6 - - + +
542G GLU* 1.3 58.1 + - + +
545G ASN* 3.6 24.1 + - - -
559G LEU* 3.8 20.4 - - - +
562G LEU* 4.6 15.0 - - - +
563G SER 5.4 0.7 - - - -
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Residues in contact with GLU 542 (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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516B PRO* 4.4 15.4 - - + +
202G ASN* 3.7 27.4 - - + +
539G LYS* 2.9 41.5 + - + +
541G MET* 1.3 77.6 - - + +
543G TRP* 1.3 57.3 + - - +
544G TRP 3.3 0.4 - - - -
545G ASN* 2.8 22.3 + - - +
546G LEU* 2.9 26.4 + - + +
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Residues in contact with TRP 543 (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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515B GLU* 3.3 38.7 + - + -
516B PRO* 4.1 12.2 - - + +
526B PHE* 4.6 2.9 - + - -
437G PRO* 3.9 13.7 - - + -
527G TYR* 3.8 20.2 - + - -
530G GLU* 3.4 35.2 - - + -
532G VAL* 3.4 7.7 - - + +
538G PHE* 3.8 32.1 - + + -
539G LYS 3.4 3.2 + - - +
540G VAL 4.2 4.0 - - - +
541G MET 3.6 0.2 - - - -
542G GLU* 1.3 77.5 - - - +
544G TRP* 1.3 108.8 + + - +
545G ASN 3.0 0.5 + - - -
546G LEU* 3.0 6.0 + - + -
547G ASN* 2.9 46.7 + - + +
551G TYR* 4.1 12.1 - + - -
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Residues in contact with TRP 544 (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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435G PHE* 3.0 30.4 + + - -
437G PRO* 3.8 3.4 - - - +
527G TYR* 3.3 31.6 - + - -
540G VAL* 3.4 25.4 + - + +
541G MET 4.4 0.4 - - - +
542G GLU 3.3 0.4 - - - -
543G TRP* 1.3 99.2 - + - +
545G ASN* 1.3 59.8 + - - +
547G ASN 3.8 1.9 - - - +
548G SER* 3.5 13.5 + - - -
551G TYR* 4.2 14.1 - + - -
554G LEU* 3.3 33.4 - - + -
555G SER* 3.2 62.1 - - - -
558G ALA* 3.4 20.3 - - + +
559G LEU* 3.8 26.0 - - + +
562G LEU* 4.3 5.4 - - + -
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Residues in contact with ASN 545 (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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199G HIS* 3.3 37.6 + - - -
201G ASN* 3.5 10.5 + - - -
202G ASN* 3.3 26.3 + - - +
541G MET 3.6 7.9 + - - +
542G GLU 2.8 12.9 + - - +
544G TRP* 1.3 76.7 - - - +
546G LEU* 1.3 65.2 + - + +
548G SER* 2.7 30.9 + - - -
559G LEU* 4.3 6.7 - - - +
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Residues in contact with LEU 546 (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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516B PRO* 4.5 14.6 - - + -
517B PRO* 4.4 20.0 - - + -
526B PHE* 4.1 13.2 - - + -
550B LYS* 3.2 47.6 + - + +
202G ASN* 5.3 3.8 - - - +
542G GLU* 2.9 22.8 + - + +
543G TRP* 3.0 8.7 + - + +
545G ASN* 1.3 83.7 - - + +
547G ASN* 1.3 61.9 + - - +
548G SER* 2.7 18.1 + - - -
549G LYS* 3.7 6.9 + - - +
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Residues in contact with ASN 547 (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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526B PHE* 3.1 39.3 - - - -
529B LYS* 5.9 0.5 - - - +
530B GLU* 5.7 0.3 - - - +
550B LYS* 4.3 4.3 + - - +
530G GLU* 3.7 15.8 - - - +
543G TRP* 2.9 39.4 + - + +
544G TRP* 3.8 5.8 - - + +
546G LEU* 1.3 72.8 - - - +
548G SER* 1.3 57.0 + - - +
549G LYS 3.1 3.1 - - - +
550G LYS* 3.7 19.3 - - + +
551G TYR* 3.0 47.9 + - + +
555G SER* 4.2 2.0 - - - -
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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