Contacts of the helix formed by residues 551 - 561 (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 TYR 551 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523G GLU* 2.9 37.7 - - + +
526G PHE* 3.8 10.7 + + + -
527G TYR* 3.6 36.5 - + + -
530G GLU* 2.6 36.6 + - - +
543G TRP* 4.1 10.1 - + - -
544G TRP* 4.2 10.1 - + + -
547G ASN* 3.0 31.7 + - + +
548G SER 3.7 3.6 - - - -
550G LYS* 1.3 100.0 + - + +
552G PRO* 1.3 66.4 - - - +
554G LEU* 3.5 17.9 - - + -
555G SER* 2.9 25.0 + - - +
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Residues in contact with PRO 552 (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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517G PRO* 6.5 0.4 - - + -
518G VAL* 4.8 15.0 - - + -
523G GLU* 3.7 11.9 - - - +
548G SER 3.6 10.4 - - - +
549G LYS* 3.1 15.7 - - - +
550G LYS 3.1 13.0 - - - +
551G TYR* 1.3 83.6 - - - +
553G LYS* 1.3 66.1 + - + +
555G SER* 3.5 3.1 + - - -
556G LYS* 3.3 26.0 - - - +
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Residues in contact with LYS 553 (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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458G MET* 3.7 33.3 - - + +
461G LEU* 4.5 7.9 - - + +
462G GLU* 3.7 37.9 + - + +
517G PRO* 5.7 7.1 - - - +
518G VAL 4.7 12.6 - - - -
520G PRO* 4.1 16.4 - - + -
523G GLU* 3.0 20.5 + - - +
552G PRO* 1.3 79.9 - - + +
554G LEU* 1.3 63.3 + - - +
555G SER 3.4 0.4 - - - -
556G LYS* 3.7 12.5 + - - +
557G LEU* 3.7 13.2 + - - +
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Residues in contact with LEU 554 (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* 4.5 20.4 - - + -
454G CYS* 5.1 0.9 - - + -
458G MET* 3.3 31.4 - - + -
523G GLU* 3.1 25.3 + - + +
524G PHE* 4.7 17.7 - - + +
527G TYR* 3.6 30.7 - - + -
544G TRP* 3.3 26.0 - - + -
551G TYR* 3.5 11.0 - - + -
553G LYS* 1.3 75.5 - - - +
555G SER* 1.3 66.4 + - - +
557G LEU* 3.3 4.7 + - + +
558G ALA* 2.9 22.0 + - - +
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Residues in contact with SER 555 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544G TRP* 3.2 43.2 - - - -
547G ASN 4.2 1.1 - - - -
548G SER* 3.5 20.3 + - - -
551G TYR 2.9 22.3 + - - -
552G PRO 3.5 5.4 + - - -
554G LEU* 1.3 77.1 - - - +
556G LYS* 1.3 63.2 + - - +
557G LEU 2.8 7.1 + - - -
558G ALA 2.9 10.0 + - - -
559G LEU* 2.9 23.3 + - - +
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Residues in contact with LYS 556 (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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172G LYS* 5.2 6.5 - - - +
461G LEU* 3.8 39.7 + - + +
464G ILE* 3.2 34.4 - - - +
552G PRO 3.3 18.1 + - - +
553G LYS* 3.7 11.0 + - - +
554G LEU 3.3 0.6 - - - -
555G SER* 1.3 84.4 + - - +
557G LEU* 1.3 55.1 + - - +
559G LEU* 4.8 5.2 - - - +
560G SER* 3.5 21.1 + - - -
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Residues in contact with LEU 557 (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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173G ASP* 5.6 2.9 - - + +
428G TRP* 5.8 0.7 - - + -
431G THR* 5.0 1.8 - - + -
435G PHE* 3.0 42.2 - - + -
453G PHE* 5.7 2.2 - - + -
454G CYS* 4.5 14.8 - - + +
457G LYS* 4.2 31.9 - - + -
458G MET* 4.7 12.3 - - + +
461G LEU* 5.0 8.5 - - + -
553G LYS 3.7 10.2 + - - +
554G LEU* 3.3 8.7 + - + +
555G SER 3.0 0.6 - - - -
556G LYS* 1.3 76.4 - - - +
558G ALA* 1.3 66.3 + - - +
559G LEU 3.1 1.8 - - - -
560G SER* 3.1 13.9 + - - +
561G LEU* 3.0 41.4 + - + +
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Residues in contact with ALA 558 (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* 3.3 26.6 - - + -
544G TRP* 3.4 43.7 - - + +
554G LEU 2.9 15.0 + - - +
555G SER 3.7 0.4 - - - +
557G LEU* 1.3 79.4 - - - +
559G LEU* 1.3 56.6 + - - +
561G LEU* 3.6 2.1 + - - +
562G LEU* 3.0 35.9 + - - +
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Residues in contact with LEU 559 (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* 3.5 46.1 - - + +
540G VAL 5.1 0.2 - - - +
541G MET* 3.8 34.3 - - - +
544G TRP* 3.8 26.5 - - + +
545G ASN* 4.3 11.4 - - - +
548G SER* 6.0 1.6 - - - -
555G SER* 2.9 24.3 + - - +
556G LYS* 4.8 5.4 - - - +
558G ALA* 1.3 74.3 - - - +
560G SER* 1.3 63.3 + - - +
561G LEU 3.0 4.3 - - - -
562G LEU* 2.9 16.8 + - + +
563G SER* 3.1 16.9 + - - -
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Residues in contact with SER 560 (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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172G LYS 4.9 0.9 - - - -
173G ASP* 2.7 29.4 + - - -
174G GLY* 3.5 14.1 - - - -
176G SER* 4.2 0.3 + - - -
199G HIS* 5.8 0.9 - - - -
244G LYS* 3.4 19.4 + - - +
428G TRP* 5.8 0.2 - - - -
556G LYS 3.5 19.0 + - - -
557G LEU* 3.1 20.4 + - - +
559G LEU* 1.3 77.3 - - - +
561G LEU* 1.3 59.4 + - - +
563G SER* 3.4 15.3 + - - -
564G ILE* 3.5 8.8 - - - +
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Residues in contact with LEU 561 (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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382G LEU* 4.2 5.6 - - + +
428G TRP* 3.3 44.9 - - + +
431G THR* 3.3 33.0 - - + -
432G ALA* 3.5 37.2 - - + +
435G PHE* 4.2 7.4 - - + -
453G PHE* 4.5 6.7 - - + -
557G LEU* 3.0 30.7 + - + +
558G ALA 3.7 4.9 - - - +
559G LEU 3.0 0.6 - - - -
560G SER* 1.3 80.0 - - - +
562G LEU* 1.3 64.9 + - + +
563G SER 3.3 2.0 - - - -
564G ILE* 3.9 19.6 + - + +
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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