Contacts of the helix formed by residues 580 - 587 (chain A) in PDB entry 3SXS
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 ALA 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A TRP 4.0 0.6 + - - -
579A SER* 1.3 75.8 - - - +
581A PRO* 1.4 72.5 - - + +
582A GLU* 3.3 30.3 - - + +
583A VAL* 3.0 18.4 + - + +
584A PHE* 3.3 9.1 + - - -
593A SER* 4.1 11.9 + - - +
596A TRP* 3.7 21.4 - - + +
656A ARG* 3.8 11.0 - - - +
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Residues in contact with PRO 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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579A SER 4.5 0.2 - - - +
580A ALA* 1.4 84.9 - - + +
582A GLU* 1.4 53.1 + - - +
583A VAL 3.1 0.2 + - - -
584A PHE* 3.4 27.1 + - + -
585A HIS* 2.8 46.9 + - + +
586A TYR* 5.3 2.5 - - + -
596A TRP* 3.3 35.7 - - + -
625A VAL* 4.3 5.8 - - + +
626A SER* 5.9 2.2 - - - +
630A ARG* 5.3 0.4 - - - +
651A GLU* 4.4 26.9 - - + +
656A ARG* 3.7 8.5 - - - +
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Residues in contact with GLU 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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566A TYR* 4.0 17.3 - - + +
580A ALA* 3.3 10.8 - - - +
581A PRO* 1.4 71.5 - - - +
583A VAL* 1.3 56.7 + - - +
586A TYR* 3.1 48.7 + - + +
587A PHE 3.1 7.1 + - - -
588A LYS* 3.1 22.8 + - + +
590A SER* 2.9 21.6 + - - +
593A SER* 2.7 23.3 + - - +
651A GLU 4.3 1.2 - - - +
653A PRO* 3.8 9.8 - - + +
656A ARG* 2.9 36.4 + - - -
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Residues in contact with VAL 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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569A SER* 3.9 14.2 - - - +
579A SER* 3.9 21.1 - - - +
580A ALA 3.0 16.9 + - - +
582A GLU* 1.3 77.0 - - + +
584A PHE* 1.3 60.7 + - - +
587A PHE* 3.2 29.3 + - - -
588A LYS 3.4 16.6 - - - +
589A TYR* 3.6 32.8 - - + +
593A SER* 3.7 17.0 - - - +
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Residues in contact with PHE 584 (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 VAL* 3.6 32.3 - - + -
579A SER* 3.5 27.4 - - - -
580A ALA 3.3 8.1 + - - -
581A PRO* 3.7 19.1 - - + -
583A VAL* 1.3 80.0 - - - +
585A HIS* 1.3 87.8 + + - +
587A PHE* 4.0 15.5 - - - -
621A VAL* 5.7 2.5 - - + -
622A VAL* 3.6 49.2 - - + +
625A VAL* 4.0 26.0 - - + -
626A SER* 3.7 5.4 - - - -
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Residues in contact with HIS 585 (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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581A PRO* 2.8 28.1 + - + +
584A PHE* 1.3 95.6 + + - +
586A TYR* 1.4 80.2 + + + +
587A PHE* 3.6 17.2 - - - -
622A VAL* 4.3 10.9 - - + +
626A SER* 2.7 32.8 + - - -
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Residues in contact with TYR 586 (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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566A TYR* 5.3 7.6 - + - -
581A PRO* 5.4 1.6 - - + -
582A GLU* 3.1 35.5 + - + +
585A HIS* 1.4 91.9 - + + +
587A PHE* 1.4 75.4 + - - +
588A LYS* 3.3 32.2 + - + +
651A GLU* 5.0 7.1 + - - -
652A LEU* 6.1 0.9 - - - +
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Residues in contact with PHE 587 (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 SER* 3.7 5.0 + - - -
569A SER* 2.9 33.1 + - - +
570A VAL* 5.8 4.5 - - + +
573A LYS* 5.5 9.2 - - - +
582A GLU 3.1 3.0 + - - -
583A VAL 3.2 17.6 + - - -
584A PHE* 4.0 13.9 - - - -
585A HIS 3.7 15.0 - - - -
586A TYR* 1.4 82.3 - - - +
588A LYS* 1.3 60.4 + - - +
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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