Contacts of the strand formed by residues 573 - 583 (chain A) in PDB entry 5UT2
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 LEU 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A GLU 3.6 7.2 - - - +
567A VAL* 3.7 28.0 - - + -
571A GLY 3.5 5.7 + - - +
572A GLN* 1.3 73.8 - - - +
574A HIS* 1.3 64.5 + - - +
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Residues in contact with HIS 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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564A ARG 3.6 0.5 - - - +
565A ARG* 3.4 3.8 - - - +
566A GLU* 2.8 39.8 + - + +
568A GLY* 3.8 18.5 + - - -
569A ASP* 4.7 2.7 - - + -
572A GLN* 3.1 43.2 + - + +
573A LEU* 1.3 76.2 - - - +
575A GLU* 1.3 65.2 + - - +
576A THR* 3.7 18.2 - - - +
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Residues in contact with GLU 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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546A ILE* 6.1 0.3 - - - +
563A VAL* 3.7 20.6 - - + +
564A ARG 3.5 4.5 - - - -
565A ARG* 3.7 35.6 + - + -
574A HIS* 1.3 77.6 - - - +
576A THR* 1.3 61.1 + - - +
577A GLU* 4.1 2.1 + - - +
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Residues in contact with THR 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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563A VAL* 3.3 4.8 - - - -
564A ARG* 2.8 38.5 + - - -
566A GLU* 2.5 31.2 + - - +
574A HIS* 3.7 13.5 - - - +
575A GLU* 1.3 73.1 - - - +
577A GLU* 1.3 76.7 + - - +
578A VAL* 3.4 10.2 + - + +
613A TYR* 4.4 15.9 - - + +
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Residues in contact with GLU 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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561A LYS* 3.5 28.6 + - - -
562A GLY 3.5 8.5 - - - +
563A VAL* 4.6 7.4 - - + +
575A GLU 4.1 2.5 + - - +
576A THR* 1.3 82.1 - - - +
578A VAL* 1.3 63.3 + - - +
613A TYR* 4.5 1.9 + - - -
628A PHE* 3.6 39.7 + - + +
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Residues in contact with VAL 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 LEU* 4.8 0.7 - - + -
561A LYS* 3.7 4.5 - - - +
562A GLY 2.9 50.1 + - - +
563A VAL 3.8 9.9 - - - +
564A ARG* 3.8 17.3 - - + +
576A THR* 3.6 10.8 - - + +
577A GLU* 1.3 81.9 - - - +
579A LEU* 1.3 59.0 + - - +
580A LEU* 3.8 24.0 - - + -
613A TYR* 3.7 26.7 - - + -
625A VAL* 3.9 9.9 - - + -
626A GLN 3.6 7.4 - - - +
628A PHE* 3.9 11.0 - - - -
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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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551A LEU* 3.6 29.2 - - + -
559A ILE* 3.6 13.9 - - + -
560A PHE 3.7 2.5 - - - +
578A VAL* 1.3 72.8 - - - +
580A LEU* 1.3 61.5 + - - +
581A LYS* 3.6 22.2 + - + -
624A LEU 3.5 3.6 - - - +
625A VAL* 3.6 2.8 - - - -
626A GLN* 2.9 62.1 + - + +
627A GLU 3.9 2.0 - - - +
628A PHE* 4.0 4.7 - - + +
903A 3YT 3.4 57.2 - - + +
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Residues in contact with LEU 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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545A LEU* 4.2 13.0 - - + -
546A ILE 3.8 17.9 - - - +
547A PHE* 3.6 49.1 - - + -
558A LYS 3.8 1.2 - - - +
559A ILE* 3.4 4.0 - - - +
560A PHE* 2.9 43.0 + - + +
561A LYS 4.6 0.9 - - - +
562A GLY* 3.8 12.3 - - - +
578A VAL* 3.8 20.4 - - + -
579A LEU* 1.3 76.0 - - - +
581A LYS* 1.3 61.5 + - - +
582A VAL* 4.0 0.8 + - - -
623A ILE* 4.1 9.2 - - + -
624A LEU 3.6 1.1 - - - -
625A VAL* 3.9 24.9 - - + -
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Residues in contact with LYS 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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557A THR* 5.5 4.0 - - + +
558A LYS 3.9 3.1 - - - -
559A ILE* 3.9 24.9 - - + -
579A LEU* 3.6 25.4 - - + +
580A LEU* 1.3 70.1 - - - +
582A VAL* 1.3 60.3 + - - +
594A PHE* 3.6 15.9 - - + -
623A ILE* 3.3 4.0 - - - -
624A LEU* 2.8 51.0 + - + +
626A GLN* 3.0 21.1 + - - +
678A ASN* 5.5 3.0 + - - -
698A SER* 3.7 10.7 + - - -
699A ASP* 2.6 36.0 + - - +
903A 3YT 4.9 6.3 + - - -
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Residues in contact with VAL 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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547A PHE* 3.6 35.2 - - + -
557A THR* 3.2 7.0 - - - -
558A LYS* 2.9 47.9 + - + +
560A PHE* 3.9 14.4 - - + -
580A LEU 4.3 2.0 - - - +
581A LYS* 1.3 74.9 - - - +
583A LEU* 1.3 74.1 - - - +
584A ASP* 3.4 1.0 + - - +
621A GLU* 5.1 5.4 - - + -
622A ASN 3.6 10.3 - - - +
623A ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 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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556A PHE* 3.5 20.9 - - + +
557A THR* 4.2 4.0 - - + -
582A VAL* 1.3 81.8 - - - +
584A ASP* 1.3 73.6 + - - +
585A LYS* 3.3 2.9 + - - -
587A HIS* 3.7 17.7 - - + +
588A ARG* 4.2 3.6 - - - -
590A TYR* 4.4 0.7 - - + -
591A SER* 3.5 41.1 - - - +
594A PHE* 3.8 24.9 - - + -
621A GLU* 5.8 0.3 - - - -
622A ASN* 2.9 36.0 + - + +
702A ILE* 3.9 26.0 - - + -
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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