Contacts of the helix formed by residues 574 - 583 (chain A) in PDB entry 6A5T
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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A ARG 5.3 2.9 - - - +
540A THR 3.9 6.7 - - - +
541A PHE* 3.5 28.5 - - + -
542A ILE* 5.2 1.3 - - - -
565A ALA* 3.7 21.5 - - + +
573A TRP* 1.3 84.8 - - - +
575A GLY* 1.3 56.4 + - - +
576A LYS* 3.1 4.5 - - - -
577A GLN* 2.6 44.5 + - - +
578A LEU* 3.7 2.9 + - - +
118H GLY 3.2 27.6 + - - +
120H LEU* 4.8 5.6 - - + -
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Residues in contact with GLY 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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535A MET* 4.1 29.4 + - - +
536A THR* 4.1 7.8 - - - +
540A THR* 4.1 16.5 + - - +
542A ILE* 4.5 8.8 - - - +
574A THR* 1.3 70.6 - - - +
576A LYS* 1.3 65.3 + - - +
578A LEU* 2.7 19.8 + - - +
579A LEU* 3.0 11.3 + - - +
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Residues in contact with LYS 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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536A THR* 4.0 25.1 - - - +
537A LEU 2.3 35.2 + - - -
538A ARG* 3.6 11.9 + - - +
574A THR* 2.8 3.0 + - - +
575A GLY* 1.3 75.3 - - - +
577A GLN* 1.3 63.3 + - - +
579A LEU* 3.5 5.1 + - + +
580A SER* 2.8 26.9 + - - -
603A ASP* 4.4 7.6 + - - -
613A VAL* 3.8 33.1 - - + +
615A PHE* 4.5 1.6 - - - +
616A GLY 3.9 24.9 - - - +
618A VAL* 6.1 0.7 - - + -
118H GLY* 4.7 3.7 + - - -
119H GLY* 3.5 36.7 - - - +
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Residues in contact with GLN 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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562A PRO* 4.0 13.2 - - + +
563A GLN 3.3 21.4 + - - +
565A ALA* 3.6 20.6 - - - +
573A TRP* 3.0 31.0 + - - -
574A THR* 2.6 28.9 + - - +
576A LYS* 1.3 74.1 - - - +
578A LEU* 1.3 62.3 + - + +
580A SER* 2.8 24.5 + - - -
581A ILE* 2.9 16.6 + - + +
613A VAL 5.8 0.7 - - - -
97H PHE* 5.6 3.6 + - - -
118H GLY* 4.5 14.4 - - - +
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Residues in contact with LEU 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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535A MET* 4.8 5.8 - - + -
542A ILE* 4.3 15.7 - - + -
547A VAL* 4.4 23.3 - - + -
550A MET* 3.5 40.8 - - + +
551A LEU* 4.4 15.3 - - + -
562A PRO* 5.0 3.6 - - + -
573A TRP* 4.7 14.8 - - + -
574A THR 4.6 4.5 - - - +
575A GLY* 2.7 14.3 + - - +
577A GLN* 1.3 76.4 - - + +
579A LEU* 1.3 54.3 + - - +
580A SER 2.6 4.5 + - - -
581A ILE* 2.2 43.3 + - + +
582A ALA* 3.4 3.5 + - - +
653A VAL* 5.1 11.8 - - + +
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Residues in contact with LEU 579 (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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532A VAL* 3.5 28.9 - - + -
535A MET* 4.3 6.7 - - + +
536A THR* 3.5 27.4 - - + -
575A GLY 3.0 13.6 + - - +
576A LYS* 3.6 5.6 - - + +
578A LEU* 1.3 74.1 - - - +
580A SER* 1.3 57.3 + - - +
582A ALA* 4.1 5.8 + - + +
583A ILE* 3.1 38.4 + - + +
613A VAL* 5.1 6.7 - - + -
618A VAL* 4.0 25.1 - - + -
650A ILE* 4.7 21.8 - - + -
653A VAL* 5.4 4.9 - - + +
654A VAL* 4.8 7.0 - - + -
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Residues in contact with SER 580 (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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576A LYS 2.8 13.3 + - - -
577A GLN* 2.8 15.3 + - - -
578A LEU 2.6 4.6 + - - -
579A LEU* 1.3 73.4 - - - +
581A ILE* 1.3 66.2 + - - +
582A ALA 3.1 2.0 - - - -
583A ILE* 3.8 11.2 + - - +
611A GLY 3.4 13.9 - - - +
612A LYS* 3.1 23.7 - - - +
613A VAL* 2.3 35.5 + - - +
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Residues in contact with ILE 581 (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 21.1 - - + -
554A VAL* 4.8 14.4 - - + +
556A SER* 5.1 3.8 + - - -
557A TRP* 3.5 36.2 - - + +
560A VAL 5.4 2.2 - - - +
562A PRO* 4.7 22.7 - - + -
577A GLN* 2.9 15.5 + - + +
578A LEU* 2.2 39.0 + - + +
580A SER* 1.3 70.7 - - - +
582A ALA* 1.3 61.8 + - - +
583A ILE 4.7 1.0 - - - +
584A PRO* 5.4 0.9 - - - +
612A LYS* 6.5 0.9 - - - -
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Residues in contact with ALA 582 (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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554A VAL* 5.0 7.7 - - + +
556A SER* 4.7 3.8 + - - -
578A LEU 3.4 3.9 + - - +
579A LEU* 4.3 9.4 - - + +
580A SER 3.1 0.8 - - - -
581A ILE* 1.3 82.1 - - - +
583A ILE* 1.3 53.8 + - + +
584A PRO* 2.8 24.7 - - - +
646A LEU* 4.7 3.1 - - + +
649A ASN* 3.5 42.5 + - + +
650A ILE* 4.4 20.0 - - + +
653A VAL* 5.4 3.8 - - + +
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Residues in contact with ILE 583 (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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579A LEU* 3.1 30.1 - - + +
580A SER* 3.8 6.5 + - - +
581A ILE 3.6 1.5 - - - +
582A ALA* 1.3 73.1 - - + +
584A PRO* 1.3 77.6 - - + +
585A SER* 3.6 0.7 + - - -
587A ILE* 4.2 22.0 - - + -
608A ILE* 4.9 11.0 - - + -
611A GLY* 3.5 27.0 - - - +
613A VAL* 4.4 19.3 - - + +
630A LEU* 4.0 33.4 - - + -
634A VAL* 4.9 1.8 - - + -
646A LEU* 4.4 7.2 - - + -
650A ILE* 5.4 4.7 - - + -
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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