Contacts of the helix formed by residues 590 - 604 (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 TYR 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A PHE* 3.3 33.7 - + - -
583A LEU* 4.0 4.5 - - + -
587A HIS* 2.9 27.9 + - + +
589A ASN* 1.3 99.8 + - - +
591A SER* 1.3 59.6 + - - +
592A GLU* 3.3 3.1 - - - -
593A SER* 3.1 7.8 + - - +
594A PHE* 2.8 25.8 + - - +
702A ILE* 3.7 36.8 - - + -
706A VAL* 3.6 33.1 + - + -
707A LEU* 4.5 0.9 - - + -
708A PRO* 3.6 23.6 - - - +
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Residues in contact with SER 591 (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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583A LEU* 3.5 18.8 - - - +
588A ARG 3.0 16.3 + - - -
589A ASN 3.3 2.4 + - - -
590A TYR* 1.3 76.5 - - - +
592A GLU* 1.3 65.9 + - - +
594A PHE* 3.1 3.0 + - - +
595A PHE* 2.8 32.7 + - - -
622A ASN* 4.0 23.1 - - - -
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Residues in contact with GLU 592 (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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589A ASN 4.9 3.3 + - - +
590A TYR 3.3 0.8 - - - -
591A SER* 1.3 82.3 + - - +
593A SER* 1.3 58.4 + - - +
595A PHE* 3.1 4.8 + - - +
596A GLU* 2.8 31.0 + - - +
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Residues in contact with SER 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A TYR* 3.1 9.7 + - - -
592A GLU* 1.3 79.0 - - - +
594A PHE* 1.3 63.7 + - - +
596A GLU* 3.8 7.4 - - - +
597A ALA* 3.1 24.4 + - - +
702A ILE* 3.7 7.1 - - - +
703A SER* 3.0 36.6 + - - -
706A VAL* 3.8 22.9 - - - +
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Residues in contact with PHE 594 (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* 3.6 26.2 - - + -
581A LYS* 3.6 30.5 - - + -
583A LEU* 3.8 31.9 - - + -
590A TYR 2.8 13.7 + - - +
591A SER* 3.3 9.6 - - - +
593A SER* 1.3 78.8 - - - +
595A PHE* 1.3 97.6 + + - +
597A ALA* 3.5 14.2 - - - +
598A ALA* 3.8 5.0 + - - +
622A ASN 3.7 14.6 - - - -
624A LEU* 4.1 17.9 - - + +
699A ASP* 5.3 0.9 - - - +
701A GLY* 5.5 2.6 - - - -
702A ILE* 3.9 20.8 - - + +
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Residues in contact with PHE 595 (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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537A PHE* 3.8 8.2 - + + -
591A SER* 2.8 28.2 + - - +
592A GLU* 3.9 3.1 - - - +
594A PHE* 1.3 94.0 - + - +
596A GLU* 1.3 62.0 + - - +
597A ALA 3.2 0.4 - - - -
598A ALA* 3.0 6.7 + - - +
599A SER* 2.8 27.9 + - - -
615A VAL* 3.7 32.1 - - + -
617A VAL* 3.7 19.3 - - + -
622A ASN* 3.3 46.0 - - + -
623A ILE 3.9 8.5 - - - -
624A LEU* 4.5 6.7 - - + -
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Residues in contact with GLU 596 (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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592A GLU 2.8 17.4 + - - +
593A SER* 3.2 8.7 + - - +
595A PHE* 1.3 72.7 - - - +
597A ALA* 1.3 66.6 + - - +
599A SER* 2.6 26.5 + - - +
600A MET* 2.8 12.6 + - - +
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Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A SER 3.1 7.2 + - - +
594A PHE 3.5 12.8 - - - +
596A GLU* 1.3 78.1 - - - +
598A ALA* 1.3 64.5 + - - +
600A MET* 3.1 17.6 + - - +
601A MET* 3.3 9.0 + - - +
699A ASP* 3.8 5.6 - - - +
700A PRO* 3.9 14.6 - - + +
701A GLY 3.3 43.7 - - - +
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Residues in contact with ALA 598 (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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537A PHE* 3.3 25.2 - - + -
594A PHE 3.8 2.6 + - - +
595A PHE* 3.0 8.5 + - - +
597A ALA* 1.3 78.0 - - - +
599A SER* 1.3 63.5 + - - +
601A MET 3.0 12.5 + - - -
602A SER 3.0 9.5 + - - -
612A ASN* 3.0 19.9 + - - +
624A LEU* 3.5 28.9 - - + -
699A ASP* 4.4 8.4 + - - +
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Residues in contact with SER 599 (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 VAL* 5.5 9.4 - - - -
537A PHE* 3.5 15.7 - - - -
595A PHE 2.8 16.7 + - - -
596A GLU* 2.6 28.4 + - - +
598A ALA* 1.3 70.9 - - - +
600A MET* 1.3 62.9 + - - +
602A SER* 3.0 4.2 + - - +
603A LYS* 2.9 23.4 + - - +
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Residues in contact with MET 600 (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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596A GLU 2.8 12.4 + - - +
597A ALA* 3.2 9.9 - - - +
599A SER* 1.3 80.1 + - - +
601A MET* 1.3 98.5 + - - +
603A LYS* 3.0 19.3 + - - +
604A LEU 4.3 0.7 + - - -
609A LEU* 6.0 0.2 - - + -
664A LEU* 3.7 39.5 - - + -
669A LEU* 3.6 33.1 - - + +
670A ILE 3.7 23.6 - - - +
671A HIS* 4.0 8.3 - - + +
700A PRO* 4.0 15.0 - - + -
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Residues in contact with MET 601 (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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597A ALA 3.8 4.7 - - - +
598A ALA 3.0 7.7 + - - +
600A MET* 1.3 106.0 - - - +
602A SER* 1.3 57.8 + - - +
604A LEU 3.0 19.8 + - - +
609A LEU* 3.6 38.9 - - + +
610A VAL* 3.9 16.8 - - + +
612A ASN* 4.1 9.4 - - - +
671A HIS* 3.8 12.8 - - - -
697A LEU* 3.1 30.1 - - + +
698A SER 3.6 11.9 - - - +
699A ASP* 3.5 27.1 - - + +
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Residues in contact with SER 602 (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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537A PHE* 3.5 14.1 - - - -
598A ALA 3.0 7.6 + - - -
599A SER* 3.0 6.2 + - - -
601A MET* 1.3 73.4 - - - +
603A LYS* 1.3 66.7 + - - +
604A LEU 3.2 6.8 + - - +
610A VAL 5.6 0.3 + - - -
612A ASN* 3.1 37.6 + - - +
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Residues in contact with LYS 603 (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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599A SER 2.9 9.9 + - - +
600A MET* 3.0 15.2 + - - +
602A SER* 1.3 79.9 - - - +
604A LEU* 1.3 75.0 + - + +
669A LEU* 4.4 8.3 - - + -
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Residues in contact with LEU 604 (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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600A MET 4.3 0.8 + - - +
601A MET 3.0 19.2 + - - +
602A SER* 4.1 4.7 - - - -
603A LYS* 1.3 93.5 - - + +
605A SER* 1.3 60.4 + - - +
606A HIS 4.1 1.2 + - - -
609A LEU* 4.2 8.3 - - + +
663A PHE* 3.6 29.2 - - + -
664A LEU* 4.6 3.6 - - + -
667A ASN* 3.5 44.2 - - + +
669A LEU* 3.8 20.9 - - + -
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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