Contacts of the strand formed by residues 573 - 580 (chain A) in PDB entry 1IT8
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 ARG 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 4.9 0.6 + - - -
12A ILE 5.7 2.9 + - - +
525A ASP* 3.2 35.6 + - + -
526A VAL 3.6 7.0 - - - +
527A PHE* 3.6 37.0 - - + +
528A ALA 4.3 0.2 - - - -
560A LEU* 3.4 35.4 - - + +
561A LEU* 4.0 9.7 - - - +
572A GLY* 1.3 72.5 - - - -
574A ALA* 1.3 61.8 + - - +
575A VAL 4.4 3.1 - - - +
576A LYS* 3.3 46.4 - - - +
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Residues in contact with ALA 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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526A VAL* 2.8 8.1 + - + +
528A ALA* 3.7 14.2 - - + +
531A VAL* 3.8 22.7 - - + -
559A ALA* 3.5 4.3 - - - +
560A LEU* 3.0 22.5 + - - -
561A LEU* 3.9 10.8 + - - -
566A MET* 3.7 30.2 - - + +
573A ARG* 1.3 75.2 - - - +
575A VAL* 1.3 67.8 + - + +
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Residues in contact with VAL 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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510A VAL* 4.3 8.1 - - + -
525A ASP* 3.1 8.8 - - - +
526A VAL* 3.0 46.1 + - + +
544A VAL* 3.9 21.1 - - + -
546A VAL* 4.2 9.6 - - + -
557A GLY* 4.1 9.2 - - - -
558A GLN 3.5 15.3 - - - +
559A ALA* 4.6 2.2 - - - -
560A LEU* 4.7 4.7 - - - +
566A MET* 4.2 15.5 - - + -
573A ARG* 3.4 2.1 - - - +
574A ALA* 1.3 87.5 - - + +
576A LYS* 1.3 75.9 + - - +
577A VAL* 4.2 7.6 - - + -
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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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525A ASP* 3.4 9.0 - - - +
541A TYR* 5.8 2.4 - - - -
557A GLY* 3.1 2.1 - - - -
558A GLN* 2.7 54.9 + - + +
560A LEU* 3.6 26.4 - - + +
573A ARG* 3.3 44.1 - - - +
575A VAL* 1.3 71.7 - - - +
577A VAL* 1.3 61.4 + - - +
578A ARG* 4.7 1.4 - - - +
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Residues in contact with VAL 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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520A ALA* 5.5 0.4 - - - -
523A GLY 3.2 28.2 - - - +
524A LYS 3.1 19.3 - - - +
525A ASP* 2.6 25.1 + - - +
526A VAL* 3.8 19.1 - - + +
546A VAL* 4.8 4.5 - - + -
555A ALA* 3.7 23.1 - - + -
556A THR 3.5 12.8 - - - +
557A GLY* 4.0 0.7 - - - -
575A VAL* 4.0 7.2 - - + +
576A LYS* 1.3 75.0 - - - +
578A ARG* 1.3 65.1 + - - +
579A LYS 3.9 8.7 - - - +
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Residues in contact with ARG 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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483A ARG* 4.2 4.9 - - - +
490A THR* 3.5 35.4 + - - +
491A LEU 3.7 13.0 - - - +
523A GLY 5.6 0.2 - - - -
543A GLU* 2.7 37.6 + - - -
556A THR* 2.9 16.9 + - + +
557A GLY* 3.9 12.9 - - - +
558A GLN* 3.8 31.5 + - - +
576A LYS 4.7 1.6 - - - +
577A VAL* 1.3 74.8 - - - +
579A LYS* 1.3 74.3 + - + +
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Residues in contact with LYS 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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477A LYS* 5.9 7.2 - - - -
492A GLY* 6.1 0.9 - - - -
493A ILE* 3.9 25.0 - - + +
523A GLY* 5.4 1.1 - - - -
555A ALA* 3.3 3.4 - - - +
556A THR* 2.9 32.5 + - + +
577A VAL* 4.1 2.9 - - - -
578A ARG* 1.3 91.0 + - + +
580A GLY* 1.3 75.6 + - - +
582A GLU 5.8 0.4 - - - +
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Residues in contact with GLY 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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493A ILE* 3.6 6.4 - - - +
520A ALA 3.7 4.3 - - - -
521A ARG 3.6 12.3 - - - -
523A GLY* 4.1 9.8 - - - -
554A LEU 3.6 1.6 - - - -
555A ALA* 3.4 15.0 - - - -
579A LYS* 1.3 89.7 - - - +
581A VAL* 1.3 64.6 + - - +
582A GLU 3.2 10.8 + - - +
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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