Contacts of the helix formed by residues 572 - 580 (chain F) in PDB entry 7C17
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 572 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452 G 3.1 65.0 + - - +
462 G 4.4 1.7 + - - -
562F ARG* 4.8 9.3 - - - +
571F TYR* 1.3 77.8 - - - +
573F LEU* 1.3 75.0 + - - +
574F GLU* 3.6 17.3 + - + +
575F GLU* 3.8 18.8 - - + +
576F VAL* 3.4 21.9 + - - +
584F ARG* 5.5 1.0 - - - -
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Residues in contact with LEU 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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452 G 5.5 1.1 - - + -
462 G 4.4 17.7 - - + +
472 T 4.9 5.4 - - + -
562F ARG* 3.5 30.3 - - - +
572F THR* 1.3 83.1 + - - +
574F GLU* 1.3 57.3 + - - +
576F VAL* 3.3 6.9 - - - +
577F GLY* 2.9 25.1 + - - -
582F VAL 5.6 0.2 - - - +
584F ARG* 3.7 55.2 - - + +
587F ILE* 3.8 28.6 - - + +
588F ARG* 4.4 15.0 - - + +
591F GLU* 4.0 9.2 - - - +
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Residues in contact with GLU 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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442 A 6.0 2.7 - - - -
452 G 4.6 15.1 + - + +
572F THR* 3.3 10.2 - - + +
573F LEU* 1.3 78.1 - - - +
575F GLU* 1.3 75.1 + - - +
577F GLY* 3.2 2.5 + - - -
578F LYS* 3.2 38.3 + - - +
582F VAL* 5.5 3.6 - - - +
584F ARG* 3.6 30.8 + - + +
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Residues in contact with GLU 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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452 G 4.9 2.8 + - - -
571F TYR* 3.7 31.9 - - + -
572F THR* 3.6 21.9 + - + +
573F LEU 3.4 0.4 - - - -
574F GLU* 1.3 91.0 - - - +
576F VAL* 1.3 60.6 + - - +
577F GLY 3.5 0.2 + - - -
578F LYS* 3.7 30.3 + - - +
579F GLN* 3.4 24.3 + - - +
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Residues in contact with VAL 576 (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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558F VAL* 3.8 29.6 - - + +
561F MET* 3.7 37.0 - - + +
562F ARG* 5.6 2.9 - - - -
571F TYR* 4.5 4.6 - - + +
572F THR 3.4 14.8 + - - +
573F LEU* 3.3 21.1 - - + +
575F GLU* 1.3 76.0 - - - +
577F GLY* 1.3 62.9 + - - +
579F GLN* 3.6 9.5 + - - +
580F PHE* 3.3 21.7 + - + +
581F ASP 4.0 1.6 + - - -
587F ILE* 3.8 23.0 - - + +
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Residues in contact with GLY 577 (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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573F LEU 2.9 18.2 + - - -
574F GLU 3.2 2.2 + - - -
575F GLU 3.2 0.6 - - - -
576F VAL* 1.3 77.7 - - - +
578F LYS* 1.3 63.0 + - - +
580F PHE 3.1 1.0 + - - -
581F ASP* 2.6 44.4 + - - -
582F VAL* 2.8 20.6 + - - +
587F ILE* 4.8 1.8 - - - -
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Residues in contact with LYS 578 (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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574F GLU* 3.2 25.5 + - - +
575F GLU* 3.7 30.3 + - - +
576F VAL 3.4 0.6 - - - -
577F GLY* 1.3 76.3 - - - +
579F GLN* 1.3 62.1 + - + +
582F VAL* 3.8 18.0 - - + +
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Residues in contact with GLN 579 (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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561F MET* 3.4 32.8 - - - +
571F TYR* 4.4 20.8 - - - -
575F GLU* 3.4 22.5 + - - +
576F VAL* 3.6 4.6 + - - +
577F GLY 3.2 0.4 - - - -
578F LYS* 1.3 81.1 - - + +
580F PHE* 1.3 81.5 + - + +
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Residues in contact with PHE 580 (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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554F ARG* 4.8 27.2 + - + +
557F LYS* 3.7 40.4 - - + -
558F VAL* 4.2 19.3 - - + -
561F MET* 4.8 6.3 - - + -
576F VAL* 3.3 11.7 + - + +
577F GLY 3.1 3.3 + - - -
579F GLN* 1.3 107.8 - - + +
581F ASP* 1.3 79.7 + - + +
582F VAL* 4.0 3.2 + - - +
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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