Contacts of the helix formed by residues 589 - 599 (chain A) in PDB entry 1F9O
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 GLU 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.6 28.9 - - - +
41A LEU* 3.9 15.9 + - + +
587A ASP* 3.0 13.7 + - - +
588A PRO* 1.3 80.8 - - + +
590A TRP* 1.3 63.8 + - - +
591A GLN 3.6 0.9 - - - -
592A THR* 3.5 14.6 + - + +
593A MET* 3.0 23.4 + - - +
604A THR 5.1 0.9 - - - +
605A GLN* 3.0 34.6 + - - +
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Residues in contact with TRP 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.8 9.9 - - + -
550A PHE* 3.7 23.8 - + - -
551A LEU* 4.1 15.3 - - + -
578A ILE* 3.4 33.4 - - + -
584A TYR* 3.3 26.9 - - + +
585A LYS* 3.6 37.7 - - + +
587A ASP* 3.0 20.5 + - + +
588A PRO 3.4 0.2 - - - -
589A GLU* 1.3 77.5 - - - +
591A GLN* 1.3 77.7 + - + +
593A MET* 3.1 36.6 + - + +
594A VAL* 2.9 45.4 + - + +
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Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A LYS 5.3 4.4 + - - +
587A ASP 4.7 1.8 + - - +
588A PRO 4.9 3.0 + - - +
589A GLU 3.6 0.4 - - - -
590A TRP* 1.3 89.6 - - + +
592A THR* 1.3 59.0 + - - +
594A VAL* 3.4 7.2 + - - +
595A ALA* 2.9 33.4 + - - +
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Residues in contact with THR 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A PRO 4.8 6.1 + - - -
589A GLU* 3.5 15.8 + - + +
590A TRP 3.2 0.4 - - - -
591A GLN* 1.3 77.6 - - - +
593A MET* 1.3 62.7 + - - +
595A ALA* 4.0 5.5 - - - +
596A ALA* 3.4 21.7 + - - +
604A THR 6.0 2.0 - - - +
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Residues in contact with MET 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.7 18.8 - - + -
547A TYR* 4.0 19.3 - - + -
550A PHE* 3.5 31.0 - - + -
551A LEU* 5.8 0.2 - - + -
589A GLU 3.0 18.5 + - - +
590A TRP* 3.1 43.7 + - + +
592A THR* 1.3 79.5 - - - +
594A VAL* 1.3 64.5 + - + +
596A ALA* 3.4 6.2 + - - +
597A LEU* 3.3 39.1 + - + +
603A PRO* 4.0 14.7 - - + +
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Residues in contact with VAL 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 4.7 17.5 - - + -
590A TRP* 2.9 53.2 + - + +
591A GLN* 4.0 9.0 - - - +
593A MET* 1.3 81.6 - - + +
595A ALA* 1.3 67.7 + - - +
597A LEU* 3.1 7.4 + - - +
598A GLN* 2.9 40.6 + - + +
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Residues in contact with ALA 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A GLN 2.9 21.5 + - - +
592A THR* 4.0 6.7 - - - +
594A VAL* 1.3 74.2 - - - +
596A ALA* 1.3 62.9 + - - +
598A GLN* 3.4 7.9 + - - +
599A ALA* 3.1 24.8 + - - +
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Residues in contact with ALA 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A THR 3.4 9.9 + - - +
593A MET 3.4 10.0 + - - +
594A VAL 3.2 0.4 - - - -
595A ALA* 1.3 77.8 - - - +
597A LEU* 1.3 58.2 + - - +
599A ALA* 3.4 1.9 + - - -
600A GLY 3.2 4.0 + - - -
601A GLN* 2.7 62.4 + - + +
602A VAL 5.0 0.4 - - - +
603A PRO* 4.3 18.2 - - + -
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A TYR 3.9 18.4 - - - +
548A HIS* 4.0 28.7 - - + +
551A LEU* 4.2 25.1 - - + -
593A MET* 3.3 23.7 + - - +
594A VAL* 3.1 9.5 + - - +
596A ALA* 1.3 78.0 - - - +
598A GLN* 1.3 62.9 + - - +
600A GLY* 2.8 24.9 + - - -
601A GLN 4.0 5.8 - - - +
603A PRO* 3.9 26.2 - - + -
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Residues in contact with GLN 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 4.6 18.4 - - - +
594A VAL* 2.9 32.3 + - + +
595A ALA* 3.7 7.4 - - - +
597A LEU* 1.3 80.6 - - - +
599A ALA* 1.3 57.2 + - - +
600A GLY 3.2 3.5 + - - -
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Residues in contact with ALA 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A ALA 3.1 17.0 + - - +
596A ALA 4.0 3.6 - - - +
597A LEU 3.2 0.4 - - - -
598A GLN* 1.3 74.3 - - - +
600A GLY* 1.3 62.0 + - - +
601A GLN* 3.4 22.4 + - - +
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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