Contacts of the helix formed by residues 568 - 578 (chain A) in PDB entry 4FUL
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 568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A PRO 3.9 2.5 + - - -
567A LEU* 1.3 75.1 - - - +
569A ALA* 1.4 62.6 + - - +
570A GLU* 3.2 36.6 - - + +
571A ASP* 3.0 24.0 + - - +
572A LYS* 2.9 27.6 + - - +
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Residues in contact with ALA 569 (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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567A LEU 4.1 0.2 + - - -
568A THR* 1.4 73.9 - - - +
570A GLU* 1.4 58.7 + - - +
572A LYS* 3.2 14.9 + - - +
573A GLU* 2.8 46.9 + - + +
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Residues in contact with GLU 570 (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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568A THR* 3.2 21.7 - - + +
569A ALA* 1.4 77.4 - - - +
571A ASP* 1.3 69.4 + - - +
573A GLU* 3.5 9.6 + - - +
574A LEU* 3.1 25.3 + - - +
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Residues in contact with ASP 571 (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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558A ILE* 3.9 30.6 - - + +
565A ASN* 5.9 0.2 + - - -
566A PRO 4.1 4.9 - - - +
567A LEU* 3.8 22.1 - - + +
568A THR* 3.0 37.2 + - - +
570A GLU* 1.3 78.4 - - - +
572A LYS* 1.3 58.3 + - - +
574A LEU* 3.4 3.0 + - - +
575A LEU* 2.9 35.5 + - - +
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Residues in contact with LYS 572 (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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392A GLN* 5.3 8.6 - - - +
567A LEU* 3.7 37.5 + - + -
568A THR 2.9 16.0 + - - +
569A ALA* 3.6 13.6 - - - +
571A ASP* 1.3 75.0 - - - +
573A GLU* 1.3 52.0 + - + +
575A LEU* 3.4 0.7 + - - -
576A TRP* 2.8 33.4 + - - +
594A SER* 3.5 22.9 - - - +
595A SER* 3.2 35.8 - - - +
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Residues in contact with GLU 573 (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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569A ALA* 2.8 30.3 + - + +
570A GLU* 3.7 8.3 - - - +
572A LYS* 1.3 72.7 - - + +
574A LEU* 1.4 52.4 + - - +
576A TRP* 3.3 5.8 + - - +
577A HIS* 2.7 38.2 + - - +
597A LYS* 6.0 6.5 - - - -
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Residues in contact with LEU 574 (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* 4.0 26.5 - - + +
554A GLN* 3.9 14.6 - - + -
555A LEU* 3.8 27.0 - - + +
558A ILE* 3.7 24.0 - - + -
570A GLU 3.1 18.0 + - - +
571A ASP* 3.7 4.0 - - - +
573A GLU* 1.4 71.9 - - - +
575A LEU* 1.3 58.7 + - - +
577A HIS* 4.7 1.8 - - - -
578A PHE* 3.0 66.7 + - + +
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Residues in contact with LEU 575 (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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555A LEU* 3.8 17.2 - - + +
558A ILE* 3.8 26.2 - - + -
559A ILE* 4.5 11.4 - - + -
567A LEU* 3.9 8.3 - - + -
571A ASP 2.9 18.8 + - - +
574A LEU* 1.3 74.8 - - - +
576A TRP* 1.4 55.7 + - - +
579A ARG 3.2 13.5 + - - -
582A SER* 3.1 35.1 + - - +
588A ALA* 4.6 3.4 - - + -
591A LYS* 3.6 19.5 - - + +
592A LEU* 3.3 28.6 - - + +
595A SER* 3.4 25.8 - - - +
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Residues in contact with TRP 576 (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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572A LYS 2.8 18.5 + - - +
573A GLU* 3.8 4.7 - - - +
575A LEU* 1.4 72.8 - - - +
577A HIS* 1.4 66.1 + - - +
578A PHE 3.2 1.6 - - - -
579A ARG* 2.9 86.3 + - + +
592A LEU* 4.6 7.2 - - + -
595A SER* 4.2 14.3 - - - +
596A VAL* 4.0 21.8 - - + -
597A LYS* 6.1 6.1 - - + -
603A ILE* 3.9 30.9 - - + +
606A LYS* 3.8 28.6 - - + +
607A THR* 3.6 32.3 - - - -
610A LEU* 4.9 4.3 - - + -
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Residues in contact with HIS 577 (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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573A GLU 2.7 22.0 + - - +
574A LEU* 4.7 1.1 - - - -
576A TRP* 1.4 74.7 - - - +
578A PHE* 1.4 96.1 + + + +
579A ARG* 3.3 19.6 + - - +
580A TYR* 5.2 1.7 + - - -
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Residues in contact with PHE 578 (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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545A ALA 5.0 8.7 - - - -
546A GLU 5.4 0.7 - - - -
547A MET* 3.4 55.9 - - + -
548A PRO* 4.5 4.3 - - + -
551A LEU* 3.7 32.5 - - + -
555A LEU* 4.1 5.2 - - + -
574A LEU* 3.0 34.1 + - + +
575A LEU 3.5 5.8 - - - -
577A HIS* 1.4 105.1 - + + +
579A ARG* 1.3 62.5 + - - +
580A TYR 3.3 2.7 - - - -
581A GLU* 2.9 16.5 + - + -
582A SER* 3.0 12.0 + - - -
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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
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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