Contacts of the helix formed by residues 551 - 563 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523H GLU* 2.8 33.6 - - + +
526H PHE* 3.4 14.6 + - + -
527H TYR* 3.4 32.9 - + + -
530H GLU* 2.5 32.6 + - - -
543H TRP* 4.2 13.2 - + - -
544H TRP* 4.3 7.6 - + + -
547H ASN* 3.0 23.3 + - + +
548H SER 3.3 4.7 - - - -
550H LYS* 1.3 118.8 - - + +
552H PRO* 1.3 58.1 - - - +
554H LEU* 3.8 20.0 - - + -
555H SER* 2.6 37.7 + - - +
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Residues in contact with PRO 552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514H ARG* 3.7 19.5 - - + +
523H GLU* 3.7 10.5 - - - +
548H SER 3.0 11.8 - - - +
549H LYS* 3.3 13.9 - - - +
550H LYS 3.1 12.1 - - - +
551H TYR* 1.3 91.3 - - - +
553H LYS* 1.3 67.5 + - + +
555H SER* 3.6 1.8 + - - +
556H LYS* 3.6 25.1 + - - +
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Residues in contact with LYS 553 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H MET* 3.7 28.3 - - + +
461H LEU* 4.8 5.6 - - + +
462H GLU* 3.7 36.3 + - + +
517H PRO* 4.9 13.3 - - - +
518H VAL 4.2 16.2 - - - +
519H CYS* 5.4 0.4 - - - +
520H PRO* 4.7 14.4 - - + -
523H GLU* 3.0 17.4 + - - +
552H PRO* 1.3 85.3 - - + +
554H LEU* 1.3 63.7 + - - +
556H LYS* 3.7 12.5 + - - +
557H LEU 3.6 11.1 + - - -
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Residues in contact with LEU 554 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H PHE* 4.1 21.5 - - + -
454H CYS* 4.9 4.0 - - + -
458H MET* 3.6 29.8 - - + -
523H GLU* 2.7 33.4 + - + +
524H PHE* 4.2 12.8 - - + +
527H TYR* 3.8 33.0 - - + -
544H TRP* 3.9 19.5 - - + -
551H TYR* 3.8 12.1 - - + -
553H LYS* 1.3 69.9 - - - +
555H SER* 1.3 67.3 + - - +
556H LYS 3.1 1.1 - - - -
557H LEU* 2.8 20.6 + - + +
558H ALA* 3.0 10.6 + - - +
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Residues in contact with SER 555 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544H TRP* 3.5 45.1 - - - -
547H ASN 4.8 0.2 - - - -
548H SER* 3.3 23.6 + - - -
551H TYR* 2.6 27.5 + - - +
552H PRO* 3.6 5.0 + - - +
554H LEU* 1.3 71.0 - - - +
556H LYS* 1.3 66.0 + - - +
558H ALA* 3.1 0.7 + - - -
559H LEU* 2.9 32.4 + - - +
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Residues in contact with LYS 556 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H LYS* 6.0 2.4 - - - +
461H LEU* 3.7 47.0 + - + +
464H ILE* 5.5 2.4 - - - +
552H PRO 3.6 16.0 + - - +
553H LYS* 3.9 11.4 - - - +
554H LEU 3.1 0.8 - - - -
555H SER* 1.3 81.4 + - - +
557H LEU* 1.3 62.3 + - - +
559H LEU* 3.5 5.9 + - - +
560H SER* 3.2 21.7 + - - -
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Residues in contact with LEU 557 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H PHE* 3.8 26.0 - - + -
453H PHE* 5.3 2.0 - - + -
454H CYS* 4.1 31.9 - - + +
457H LYS* 4.1 25.1 - - + -
458H MET* 4.4 8.7 - - + +
461H LEU* 4.3 9.3 - - + +
553H LYS 3.6 8.7 + - - +
554H LEU* 2.8 20.6 + - + +
556H LYS* 1.3 74.0 - - - +
558H ALA* 1.3 60.5 + - - +
560H SER* 2.5 24.3 + - - +
561H LEU* 3.1 33.1 + - + +
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Residues in contact with ALA 558 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H PHE* 3.9 23.8 - - + -
544H TRP* 3.4 52.0 - - + +
554H LEU 3.0 9.0 + - - +
555H SER 3.1 2.0 + - - +
557H LEU* 1.3 75.3 - - - +
559H LEU* 1.3 58.3 + - - +
561H LEU* 3.2 1.2 + - - +
562H LEU* 2.8 36.8 + - - +
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Residues in contact with LEU 559 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H HIS* 3.7 31.3 - - + +
541H MET* 3.8 30.4 - - + +
544H TRP* 3.6 28.9 - - + -
545H ASN* 3.6 35.0 - - - +
548H SER* 6.1 1.1 - - - -
555H SER* 2.9 22.1 + - - +
556H LYS* 4.0 4.3 - - - +
558H ALA* 1.3 73.6 - - - +
560H SER* 1.3 58.7 + - - +
561H LEU 3.0 6.4 + - - -
562H LEU* 3.8 4.9 - - + +
563H SER* 3.0 25.6 + - - -
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Residues in contact with SER 560 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H LYS 5.3 0.9 - - - -
173H ASP 3.2 26.2 + - - -
174H GLY* 3.6 12.8 - - - -
199H HIS* 5.6 1.6 - - - -
244H LYS* 2.9 25.2 + - - +
461H LEU* 5.6 2.6 - - - +
556H LYS 3.2 12.2 + - - -
557H LEU* 2.5 35.0 + - - +
559H LEU* 1.3 76.2 - - - +
561H LEU* 1.3 57.5 + - - +
563H SER* 3.4 15.9 + - - -
564H ILE* 3.5 4.0 - - - +
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Residues in contact with LEU 561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H LYS* 5.7 0.2 - - - +
382H LEU* 4.4 6.6 - - + +
428H TRP* 3.2 45.3 - - + +
431H THR* 3.7 13.7 - - + -
432H ALA* 3.6 30.0 - - + +
435H PHE* 3.6 29.8 - - + -
453H PHE* 4.5 4.3 - - + -
557H LEU* 3.1 31.9 + - + +
558H ALA 3.7 4.0 - - - +
559H LEU 3.1 0.2 - - - -
560H SER* 1.3 78.7 - - - +
562H LEU* 1.3 59.5 + - - +
563H SER 3.0 4.5 - - - -
564H ILE* 2.9 32.4 + - + +
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Residues in contact with LEU 562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H LEU* 5.0 0.6 - - - +
380H PRO* 2.9 41.8 - - + +
381H SER 4.2 0.5 + - - -
382H LEU* 5.2 1.9 + - - -
383H CYS* 3.9 32.5 - - + +
432H ALA* 4.5 7.0 - - - +
435H PHE* 4.2 13.0 - - + +
540H VAL* 3.2 35.7 - - + -
541H MET* 4.7 4.3 - - + -
544H TRP* 3.6 24.5 - - + +
558H ALA* 2.8 25.0 + - + +
559H LEU* 3.8 11.0 - - + +
561H LEU* 1.3 75.6 - - + +
563H SER* 1.3 57.4 + - - +
564H ILE 3.2 6.7 + - - +
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Residues in contact with SER 563 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H GLY 3.6 17.2 + - - -
176H SER* 3.7 5.4 + - - -
197H HIS* 3.7 13.0 - - - +
198H TYR* 3.8 16.7 - - - -
199H HIS* 4.1 4.0 + - - -
204H LEU* 3.6 31.8 - - - +
541H MET* 5.8 0.4 - - - -
559H LEU 3.0 14.2 + - - -
560H SER* 3.4 16.1 + - - -
561H LEU 3.0 0.4 - - - -
562H LEU* 1.3 76.2 - - - +
564H ILE* 1.3 61.6 + - - +
565H PRO* 3.3 9.2 - - - +
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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