Contacts of the helix formed by residues 548 - 563 (chain F) in PDB entry 5G04
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 548 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516F MET* 5.4 6.4 - - - +
519F GLU* 3.6 29.3 + - + +
543F LEU* 3.0 25.4 + - + +
546F LEU* 3.0 22.9 + - + +
547F GLN* 1.3 73.8 - - - +
549F ASP* 1.3 57.0 + - - +
550F VAL* 3.3 7.4 - - + -
551F ALA* 3.2 23.4 + - + -
552F LEU* 2.9 31.0 + - - +
579F LEU* 4.3 1.1 - - - +
286K TYR* 5.3 2.6 + - - -
290K LYS* 5.0 15.0 - - - +
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Residues in contact with ASP 549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547F GLN* 2.7 33.2 + - - +
548F LYS* 1.3 71.6 - - - +
550F VAL* 1.3 57.4 + - - +
552F LEU* 3.7 1.6 + - - +
553F SER* 3.1 24.3 + - - -
576F CYS* 4.5 2.6 - - - -
579F LEU* 3.0 27.5 - - - +
580F GLN* 3.6 32.3 + - - +
581F ARG* 5.7 2.8 + - - -
60M LEU* 3.5 23.4 - - + +
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Residues in contact with VAL 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F LYS* 5.0 4.5 - - + -
549F ASP* 1.3 79.1 - - - +
551F ALA* 1.3 67.9 + - + +
553F SER* 3.3 11.2 + - - -
554F VAL* 3.2 21.1 - - + +
285K PHE* 4.0 8.3 - - + -
286K TYR* 5.2 4.3 - - + -
289K HIS* 3.0 57.4 - - + +
290K LYS* 4.9 14.6 - - - +
60M LEU* 3.7 10.5 - - + +
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Residues in contact with ALA 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519F GLU* 6.1 0.2 - - - +
539F TYR* 5.4 3.1 + - - +
543F LEU* 4.1 14.8 - - + +
548F LYS* 3.2 33.8 + - + +
550F VAL* 1.3 82.7 - - + +
552F LEU* 1.3 62.2 + - - +
554F VAL* 3.5 5.2 + - - +
555F LEU* 3.2 19.2 + - - +
286K TYR* 4.2 24.9 - - + +
290K LYS* 5.5 0.7 - - - +
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Residues in contact with LEU 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F SER* 3.6 35.2 - - - +
543F LEU* 3.5 25.5 - - + +
544F TRP* 4.4 7.0 - - + +
548F LYS 2.9 16.3 + - - +
549F ASP 4.0 3.4 - - - +
551F ALA* 1.3 78.5 - - - +
553F SER* 1.3 56.4 + - - +
555F LEU* 3.1 10.7 + - + +
556F SER* 2.9 28.9 + - - -
572F ALA 4.3 7.0 - - - +
575F ASN* 3.9 8.7 - - + +
576F CYS* 3.7 30.1 - - - +
579F LEU* 3.6 27.4 - - + -
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Residues in contact with SER 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549F ASP 3.1 14.9 + - - -
550F VAL 3.3 9.9 + - - -
551F ALA 3.4 0.2 - - - -
552F LEU* 1.3 71.3 - - - +
554F VAL* 1.3 67.3 + - - +
556F SER* 3.9 0.5 - - - -
557F LYS* 3.1 31.3 + - - +
576F CYS* 3.2 22.6 - - - -
285K PHE* 3.7 5.5 - - - -
60M LEU* 2.9 43.4 + - - -
61M ALA 5.2 0.2 - - - -
62M LEU* 4.4 3.6 - - - -
65M LEU* 5.8 0.2 - - - -
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Residues in contact with VAL 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550F VAL 3.2 11.4 + - - +
551F ALA 3.6 6.3 - - - +
552F LEU 3.3 0.2 - - - -
553F SER* 1.3 75.4 + - - +
555F LEU* 1.3 51.4 + - - +
557F LYS* 4.1 4.6 - - - +
558F ASP* 2.8 43.9 + - + +
282K ASN* 3.9 30.8 - - + +
285K PHE* 3.1 34.3 - - + -
286K TYR* 3.5 32.3 - - + -
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Residues in contact with LEU 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526F ARG* 3.8 24.5 - - - +
536F MET* 4.4 4.3 - - + +
539F TYR* 4.0 24.5 - - + -
540F SER* 3.7 34.5 - - - -
543F LEU* 3.9 10.1 - - + -
551F ALA 3.2 9.1 + - - +
552F LEU* 3.1 21.9 + - + +
554F VAL* 1.3 79.3 - - - +
556F SER* 1.3 57.7 + - - +
558F ASP* 3.3 5.5 - - - +
559F LEU* 2.8 45.6 + - + +
572F ALA* 4.0 11.2 - - + -
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Residues in contact with SER 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F LEU* 2.9 15.7 + - - +
553F SER 3.2 4.0 + - - -
555F LEU* 1.3 76.0 - - - +
557F LYS* 1.3 65.0 + - - +
559F LEU* 4.2 0.6 - - - +
560F THR* 3.0 30.8 + - - -
569F ALA 5.1 0.2 - - - +
572F ALA* 3.0 30.4 + - - +
573F ALA* 3.1 23.0 - - - +
576F CYS* 3.8 14.1 - - - +
65M LEU* 4.1 8.9 - - - +
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Residues in contact with LYS 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F SER* 3.1 21.7 + - - +
554F VAL* 4.6 2.1 - - - +
556F SER* 1.3 75.9 - - - +
558F ASP* 1.3 55.9 + - - +
561F ASP* 3.0 47.3 + - - +
281K ALA* 5.2 1.6 - - - +
282K ASN* 3.0 26.3 + - - +
285K PHE* 3.9 33.8 - - + +
308K TYR* 4.0 8.2 + - - -
60M LEU 4.2 4.9 - - - +
61M ALA* 3.6 24.7 - - + +
63M GLN 4.5 0.4 - - - +
64M TYR* 3.7 32.8 - - + +
65M LEU* 4.0 18.3 - - + +
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Residues in contact with ASP 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526F ARG* 2.7 34.0 + - - +
554F VAL* 2.8 27.9 + - + +
555F LEU* 3.3 6.9 - - - +
556F SER 3.1 0.2 - - - -
557F LYS* 1.3 74.0 - - - +
559F LEU* 1.3 65.2 + - - +
561F ASP* 4.2 0.9 - - - +
562F MET* 3.2 26.9 + - - +
59H ARG* 5.4 4.2 + - - -
282K ASN* 3.7 27.6 + - - +
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Residues in contact with LEU 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526F ARG* 3.9 27.1 - - - +
532F ARG 4.8 2.5 - - - +
533F VAL* 3.8 11.9 - - + -
536F MET* 3.8 31.6 - - + -
555F LEU* 2.8 27.2 + - + +
556F SER 4.2 1.8 - - - +
558F ASP* 1.3 73.1 - - - +
560F THR* 1.3 59.5 + - - +
562F MET* 3.1 30.2 + - + +
563F ASP* 2.8 31.8 + - - +
568F GLU 4.4 0.2 - - - +
569F ALA* 3.8 31.6 - - + +
572F ALA* 4.1 11.7 - - + -
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Residues in contact with THR 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556F SER 3.0 17.3 + - - -
557F LYS 4.5 0.4 - - - -
559F LEU* 1.3 75.8 - - - +
561F ASP* 1.3 68.9 + - - +
563F ASP 3.3 19.3 - - - +
564F LYS* 3.8 10.8 + - + +
569F ALA* 3.9 11.6 + - - +
570F TRP* 3.4 50.6 - - + -
573F ALA* 4.0 4.3 - - - +
64M TYR 5.1 2.2 - - - +
65M LEU* 4.2 13.0 - - + -
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Residues in contact with ASP 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F LYS* 3.0 32.5 + - - +
558F ASP* 4.2 2.2 - - - +
560F THR* 1.3 80.9 - - - +
562F MET* 1.3 63.5 + - - +
563F ASP* 4.3 0.5 - - - -
282K ASN* 4.8 10.9 + - - +
64M TYR* 4.0 28.2 - - - +
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Residues in contact with MET 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526F ARG* 5.6 0.7 - - - +
530F ASN 4.5 3.8 - - - +
531F TYR* 3.6 25.6 - - - +
533F VAL* 3.8 26.5 - - + -
558F ASP* 3.2 16.6 + - - +
559F LEU* 3.1 25.0 + - + +
561F ASP* 1.3 78.1 - - - +
563F ASP* 1.3 67.4 + - + +
55H TYR* 3.5 42.4 - - + +
59H ARG* 3.4 38.0 + - - +
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Residues in contact with ASP 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533F VAL* 4.8 2.1 - - - +
559F LEU 2.8 26.2 + - - +
560F THR* 3.3 13.2 - - - +
561F ASP 3.3 1.7 - - - -
562F MET* 1.3 94.5 - - + +
564F LYS* 1.3 77.0 + - - +
565F ASN 3.8 5.9 - - - +
566F SER* 2.9 29.3 + - - -
569F ALA* 3.5 9.4 - - - +
55H TYR* 3.6 33.0 + - + -
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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
------------------------------------------------------------
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