Contacts of the helix formed by residues 569 - 575 (chain F) in PDB entry 6D84
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 THR 569 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261F LYS* 5.9 1.3 - - + -
566F TYR* 3.3 43.2 - - + +
567F ILE 4.4 3.1 - - - +
568F GLY* 1.3 77.6 - - - +
570F LEU* 1.3 63.5 + - - +
571F ALA* 3.3 3.5 + - - +
572F SER* 2.3 45.3 + - - -
573F VAL* 3.2 11.3 + - - +
74P ASN* 3.3 18.2 - - - +
75P ALA 3.8 6.7 - - - +
76P CYS* 5.2 7.0 - - + -
77P VAL* 3.5 5.6 - - - -
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Residues in contact with LEU 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569F THR* 1.3 71.9 - - - +
571F ALA* 1.3 55.0 + - - +
573F VAL* 3.5 3.8 + - - +
574F TYR* 3.0 39.4 + - + +
581F PHE* 3.6 19.7 - - + -
49P ILE* 4.3 31.0 - - + -
56P ARG* 3.8 26.5 - - + -
58P MET* 4.3 9.0 - - - -
71P SER* 5.3 0.7 - - - +
72P LYS 5.4 0.4 - - - +
73P LYS 3.3 26.5 - - - +
74P ASN* 2.7 18.8 + - - +
75P ALA* 3.7 11.7 - - + +
77P VAL* 3.4 20.9 - - + +
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Residues in contact with ALA 571 (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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563F LEU* 4.2 4.9 - - + +
566F TYR* 4.5 5.6 - - + -
569F THR* 3.2 8.6 + - - +
570F LEU* 1.3 77.0 - - - +
572F SER* 1.3 58.5 + - - +
573F VAL 3.3 0.2 - - - -
574F TYR* 4.5 1.3 - - - +
575F HIS* 3.0 24.8 + - - -
576F LYS 3.3 25.6 + - - +
578F PRO* 3.8 22.9 - - + -
581F PHE* 3.3 23.9 - - + -
74P ASN* 3.7 2.4 + - - +
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Residues in contact with SER 572 (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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304F ARG* 4.1 4.4 - - - +
305F ASN* 3.3 25.1 + - - +
308F LEU* 4.2 8.3 - - - +
563F LEU* 5.3 0.2 - - - -
566F TYR 3.2 24.6 + - - -
567F ILE* 3.7 0.2 - - - -
568F GLY* 3.0 12.4 + - - -
569F THR* 2.3 42.0 + - - -
571F ALA* 1.3 76.3 - - - +
573F VAL* 1.3 66.3 + - - +
575F HIS* 3.8 21.3 + - - -
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Residues in contact with VAL 573 (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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300F TYR* 3.8 28.3 - - + +
301F VAL* 3.7 36.8 - - + -
304F ARG* 2.8 45.4 + - + +
569F THR 3.2 14.9 + - - +
570F LEU* 3.8 7.4 - - - +
572F SER* 1.3 76.3 + - - +
574F TYR* 1.3 73.3 + - + +
575F HIS* 3.2 4.2 + - - -
49P ILE* 4.0 19.1 - - + -
77P VAL* 4.5 3.1 - - + -
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Residues in contact with TYR 574 (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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300F TYR* 5.8 2.2 - - - -
304F ARG* 4.1 9.7 + - - +
570F LEU* 3.0 26.2 + - + +
571F ALA* 4.4 0.9 - - - +
573F VAL* 1.3 90.5 - - + +
575F HIS* 1.3 68.2 + - - +
576F LYS* 3.2 45.7 + - + +
581F PHE* 4.1 22.7 - + + -
49P ILE* 3.4 22.1 + - + +
51P ALA* 4.6 5.2 - - - +
56P ARG* 2.9 48.3 + - - -
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Residues in contact with HIS 575 (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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304F ARG* 3.1 53.9 + - - +
307F ASN* 4.1 17.0 + - + +
308F LEU* 3.7 29.9 - - + +
311F GLN* 5.4 0.2 - - - -
555F ILE* 3.8 29.7 - - + +
559F LEU* 5.2 5.9 - - - +
563F LEU* 3.7 12.6 - - - +
571F ALA 3.0 10.1 + - - -
572F SER 3.8 8.5 + - - -
573F VAL 3.2 21.0 + - - -
574F TYR* 1.3 77.3 - - - +
576F LYS* 1.3 58.7 + - - +
577F PRO* 5.0 0.3 - - - +
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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