Contacts of the helix formed by residues 506 - 516 (chain F) in PDB entry 4P0S
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 SER 506 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482F TRP* 3.9 5.0 - - - +
504F TYR 2.7 14.9 + - - +
505F PRO* 1.3 79.5 - - - +
507F PRO* 1.3 75.0 - - - +
508F GLN* 3.2 8.5 + - - +
509F LEU* 3.2 38.1 + - - +
510F LEU 3.4 7.6 + - - -
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Residues in contact with PRO 507 (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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482F TRP* 3.5 50.0 - - + -
485F GLN* 5.5 0.7 - - - +
506F SER* 1.3 87.3 - - - +
508F GLN* 1.3 65.5 + - + +
510F LEU* 3.2 3.8 + - - +
511F VAL* 3.0 24.5 + - - +
557F MET* 5.7 4.9 - - + -
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Residues in contact with GLN 508 (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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547E TYR 5.8 3.4 - - - +
506F SER* 3.1 8.9 + - - +
507F PRO* 1.3 81.4 - - + +
509F LEU* 1.3 64.5 + - + +
511F VAL* 2.9 30.7 - - - +
512F GLN* 3.0 35.4 + - - +
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Residues in contact with LEU 509 (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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503F ALA 5.8 0.4 - - - +
504F TYR* 3.8 18.0 - - + -
505F PRO* 4.1 25.6 - - + -
506F SER* 3.2 24.0 + - - +
508F GLN* 1.3 78.8 - - + +
510F LEU* 1.3 56.6 + - - +
512F GLN* 3.6 21.9 - - - +
513F ALA* 3.2 24.1 + - - +
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Residues in contact with LEU 510 (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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482F TRP* 4.4 21.5 - - + -
500F VAL* 5.6 5.2 - - + -
504F TYR* 3.9 30.5 - - + -
506F SER 3.4 5.3 + - - +
507F PRO 3.2 9.6 + - - +
508F GLN 3.1 0.6 - - - -
509F LEU* 1.3 75.6 - - - +
511F VAL* 1.3 65.1 + - - +
512F GLN 3.2 1.3 - - - -
513F ALA 3.1 9.0 + - - -
514F TYR* 3.3 45.0 + - + +
526F LEU* 4.0 18.8 - - + -
527F LEU* 4.8 5.6 - - + -
553F ILE* 4.9 13.9 - - + -
557F MET* 4.9 12.1 - - + -
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Residues in contact with VAL 511 (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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507F PRO 3.0 15.4 + - - +
508F GLN* 2.9 37.9 - - - +
510F LEU* 1.3 76.0 - - - +
512F GLN* 1.3 64.2 + - + +
514F TYR* 3.3 13.7 + - + +
515F GLN* 3.2 36.8 + - + +
557F MET 6.0 1.6 - - - +
558F THR* 6.1 4.7 - - + -
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Residues in contact with GLN 512 (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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508F GLN* 3.0 49.8 + - - +
509F LEU* 3.6 22.6 - - - +
511F VAL* 1.3 82.4 - - + +
513F ALA* 1.3 54.9 + - - +
515F GLN* 3.3 22.2 + - - +
516F GLN* 2.9 36.5 + - - +
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Residues in contact with ALA 513 (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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504F TYR* 3.6 37.2 - - + +
509F LEU 3.2 7.4 + - - +
510F LEU 3.1 10.8 + - - +
512F GLN* 1.3 72.1 - - - +
514F TYR* 1.3 62.7 + - - +
516F GLN* 3.1 35.6 + - - +
517F CYS* 3.3 12.8 + - - -
526F LEU* 4.3 14.2 - - + +
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Residues in contact with TYR 514 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510F LEU* 3.3 47.0 + - + +
511F VAL* 3.3 11.1 + - + +
513F ALA* 1.3 74.1 - - - +
515F GLN* 1.3 63.9 + - + +
517F CYS* 3.1 6.5 + - - -
523F ARG* 2.9 73.6 + - + +
526F LEU* 3.5 19.1 - - + +
527F LEU* 4.1 18.9 - - - +
550F SER* 4.8 1.2 + - - -
553F ILE* 4.1 4.6 - - - +
554F TYR* 3.6 39.3 + + - +
557F MET* 5.2 4.7 - - + -
558F THR* 4.3 19.5 - - + -
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Residues in contact with GLN 515 (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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511F VAL* 3.2 24.1 + - + +
512F GLN* 3.3 35.9 - - - +
514F TYR* 1.3 78.1 - - + +
516F GLN* 1.3 57.5 + - - +
517F CYS 2.9 16.1 - - - +
523F ARG* 4.2 5.3 + - - +
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Residues in contact with GLN 516 (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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512F GLN* 2.9 23.3 + - + +
513F ALA* 3.1 22.4 + - - +
515F GLN* 1.3 74.0 - - + +
517F CYS* 1.3 64.1 + - - +
518F PHE* 3.1 25.5 - - - -
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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