Contacts of the helix formed by residues 625 - 637 (chain A) in PDB entry 3BWT
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 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A SER* 5.8 3.8 - - - +
594A ASP* 5.4 3.4 - - - +
623A GLU 5.6 0.7 - - - +
624A VAL* 1.3 79.2 - - - +
626A THR* 1.3 59.3 + - - +
627A GLU* 3.3 19.0 + - - +
628A GLN* 2.8 40.1 + - - +
629A ARG* 2.8 27.4 + - - +
661A LYS* 5.9 0.9 - - - +
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Residues in contact with THR 626 (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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625A THR* 1.3 73.6 - - - +
627A GLU* 1.3 78.6 + - - +
629A ARG* 3.0 27.2 + - - +
630A ILE* 2.9 49.7 + - + +
661A LYS* 3.1 19.9 + - - +
662A THR* 3.8 20.2 - - + -
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Residues in contact with GLU 627 (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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625A THR* 3.3 17.2 + - - +
626A THR* 1.3 91.4 + - - +
628A GLN* 1.3 63.5 + - + +
630A ILE* 3.3 16.7 + - + +
631A VAL* 3.3 18.0 + - - +
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Residues in contact with GLN 628 (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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593A ALA* 4.8 1.6 - - - +
594A ASP* 2.9 40.5 + - - +
597A PHE* 3.4 46.5 - - + -
598A GLU* 5.2 1.2 + - - -
624A VAL* 3.0 26.5 - - + +
625A THR* 2.8 42.3 + - - +
626A THR 3.2 0.2 - - - -
627A GLU* 1.3 76.7 - - + +
629A ARG* 1.3 65.8 + - - +
631A VAL* 2.9 11.8 + - - -
632A LEU* 3.0 11.3 + - - +
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Residues in contact with ARG 629 (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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621A LEU* 4.3 24.8 + - + +
624A VAL* 3.4 16.2 + - + +
625A THR 2.8 22.5 + - - +
626A THR* 3.0 31.1 + - - +
627A GLU 3.3 0.2 - - - -
628A GLN* 1.3 76.6 - - - +
630A ILE* 1.3 58.1 + - - +
632A LEU* 3.2 7.8 + - - +
633A THR* 2.9 35.1 + - - +
656A LEU* 5.1 0.9 - - + -
659A CYS* 3.4 39.1 + - - +
660A ILE* 3.7 4.6 - - + +
661A LYS* 3.1 38.2 - - - +
665A GLU* 2.5 37.5 + - - +
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Residues in contact with ILE 630 (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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626A THR* 2.9 37.0 + - + +
627A GLU* 3.6 9.6 - - + +
629A ARG* 1.3 76.2 - - - +
631A VAL* 1.3 58.7 + - + +
633A THR* 3.5 7.1 + - - -
634A LYS* 3.0 51.0 + - + +
662A THR* 4.4 8.7 - - + +
664A GLU* 4.0 30.3 - - + +
665A GLU* 3.7 22.2 - - + -
668A ILE* 4.8 3.8 - - + -
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Residues in contact with VAL 631 (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 PHE* 3.8 23.8 - - + -
601A LYS* 5.0 6.5 - - + +
627A GLU 3.3 14.5 + - - +
628A GLN* 2.9 8.7 + - - +
630A ILE* 1.3 76.7 - - + +
632A LEU* 1.3 65.8 + - - +
634A LYS* 3.1 9.7 + - + +
635A ILE* 3.0 43.4 + - + +
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Residues in contact with LEU 632 (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 PHE* 3.7 24.0 - - + -
601A LYS* 4.0 11.2 - - + -
604A THR* 3.5 30.8 + - + -
608A MET* 5.5 2.8 - - + +
617A ILE* 5.0 7.4 - - + -
620A LEU* 3.9 31.4 - - + -
621A LEU* 4.1 27.1 - - + -
624A VAL* 5.0 7.9 - - + -
628A GLN 3.0 15.0 + - - +
629A ARG 3.6 6.7 - - - +
631A VAL* 1.3 77.1 - - + +
633A THR* 1.3 54.3 + - - +
635A ILE* 3.5 3.9 + - + +
636A SER* 2.7 35.3 + - - -
656A LEU* 4.9 2.7 - - + -
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Residues in contact with THR 633 (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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629A ARG* 2.9 21.0 + - - +
630A ILE* 3.7 8.3 - - - -
632A LEU* 1.3 77.7 - - - +
634A LYS* 1.3 57.4 + - - +
636A SER* 3.4 5.8 + - - -
637A SER* 2.9 34.1 + - - -
640A PHE* 4.6 4.7 - - + -
656A LEU* 4.0 31.9 - - + +
660A ILE* 4.6 0.6 - - + +
665A GLU* 4.4 17.2 + - + +
668A ILE* 3.6 28.9 - - + -
669A VAL* 4.3 11.4 - - + -
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Residues in contact with LYS 634 (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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630A ILE* 3.0 36.3 + - + +
631A VAL* 3.1 9.8 + - + +
633A THR* 1.3 78.3 - - - +
635A ILE* 1.3 60.9 + - + +
637A SER* 3.1 19.4 + - - -
638A PRO* 3.4 8.5 - - - +
664A GLU* 3.9 12.9 + - - -
668A ILE* 3.7 28.9 - - + -
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Residues in contact with ILE 635 (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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601A LYS* 3.3 40.8 - - + +
602A ASP* 4.7 14.8 - - - +
604A THR* 4.0 12.6 - - + +
605A VAL* 4.4 6.6 - - + +
631A VAL* 3.0 36.0 + - + +
632A LEU* 4.0 4.0 - - - +
634A LYS* 1.3 77.2 - - + +
636A SER* 1.3 62.6 + - - +
638A PRO* 3.4 10.4 - - - +
639A HIS* 3.7 13.6 + - + -
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Residues in contact with SER 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A THR* 3.7 13.5 - - - -
605A VAL* 4.1 9.0 - - - -
608A MET* 4.1 8.6 - - - +
632A LEU 2.7 23.9 + - - -
633A THR* 3.4 6.1 + - - -
635A ILE* 1.3 79.0 - - - +
637A SER* 1.3 54.4 + - - +
638A PRO 3.3 0.4 - - - -
639A HIS* 2.7 33.3 + - - +
640A PHE* 3.4 16.8 - - - -
643A ILE* 3.9 18.5 - - - +
656A LEU* 4.0 7.8 - - - +
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Residues in contact with SER 637 (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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633A THR 2.9 16.1 + - - -
634A LYS* 3.1 13.5 + - - -
636A SER* 1.3 76.9 + - - +
638A PRO* 1.3 76.2 - - - +
639A HIS 3.1 1.2 + - - -
640A PHE* 3.4 28.4 + - - +
668A ILE* 3.8 16.5 - - - +
672A SER* 3.0 35.8 + - - +
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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