Contacts of the helix formed by residues 662 - 674 (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 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626A THR* 3.8 23.8 - - + -
629A ARG* 4.8 0.9 - - - +
630A ILE* 4.4 6.6 - - + +
660A ILE* 4.8 2.8 - - - +
661A LYS* 1.3 82.9 + - + +
663A ASP* 1.3 65.6 + - - +
664A GLU* 3.6 11.0 + - - +
665A GLU* 2.8 45.9 + - - +
666A ALA* 3.6 14.7 + - - +
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Residues in contact with ASP 663 (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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661A LYS 4.4 3.8 - - - +
662A THR* 1.3 76.9 - - - +
664A GLU* 1.3 62.2 + - - +
665A GLU 3.2 1.3 - - - -
666A ALA* 3.2 7.7 + - + +
667A GLN* 2.9 34.1 + - + +
698A LYS* 3.4 27.0 + - - -
701A ASN* 4.8 7.3 + - - +
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Residues in contact with GLU 664 (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* 4.0 27.0 - - + +
634A LYS* 3.9 24.8 + - - -
662A THR* 4.0 8.8 + - - +
663A ASP* 1.3 81.1 - - - +
665A GLU* 1.3 56.7 + - - +
667A GLN* 3.4 6.7 + - - +
668A ILE* 3.0 41.0 + - + +
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Residues in contact with GLU 665 (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* 2.5 52.9 + - - +
630A ILE* 3.7 25.7 - - + +
633A THR* 4.4 11.2 + - - +
660A ILE* 3.4 23.7 - - + +
661A LYS 3.2 0.3 + - - -
662A THR* 2.8 49.7 + - - +
664A GLU* 1.3 79.5 - - - +
666A ALA* 1.3 60.9 + - - +
668A ILE* 3.6 8.6 + - - +
669A VAL* 3.2 28.1 + - - +
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Residues in contact with ALA 666 (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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660A ILE* 4.1 16.1 - - + +
662A THR 3.6 9.3 + - - +
663A ASP* 3.2 12.3 + - - +
664A GLU 3.2 0.4 - - - -
665A GLU* 1.3 76.5 - - - +
667A GLN* 1.3 61.3 + - - +
669A VAL* 3.2 3.2 + - - +
670A VAL* 2.9 36.8 + - - +
697A LEU* 4.8 9.4 - - + -
701A ASN* 3.8 28.7 - - + +
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Residues in contact with GLN 667 (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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663A ASP* 2.9 19.4 + - + +
664A GLU* 3.8 6.5 - - - +
665A GLU 3.4 0.2 - - - -
666A ALA* 1.3 78.0 - - - +
668A ILE* 1.3 56.5 + - + +
670A VAL* 3.3 22.3 - - - +
671A ASP* 2.8 51.2 + - - +
674A ARG* 5.2 2.0 - - - +
701A ASN* 3.2 24.4 - - - +
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Residues in contact with ILE 668 (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* 4.8 4.5 - - + -
633A THR* 3.6 26.2 - - + +
634A LYS* 3.7 38.6 - - + -
637A SER* 3.8 21.1 - - - +
664A GLU* 3.0 32.2 + - + +
665A GLU* 3.8 6.5 - - - +
667A GLN* 1.3 76.4 - - + +
669A VAL* 1.3 57.1 + - - +
671A ASP* 3.9 5.9 - - - +
672A SER* 3.0 33.5 + - - +
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Residues in contact with VAL 669 (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* 4.3 5.8 - - + -
640A PHE* 4.1 15.9 - - + -
656A LEU* 4.1 26.0 - - + -
657A ILE* 4.5 11.2 - - + -
660A ILE* 4.4 11.0 - - + -
665A GLU 3.2 14.8 + - - +
666A ALA* 3.2 10.1 + - - +
668A ILE* 1.3 74.4 - - - +
670A VAL* 1.3 68.3 + - - +
672A SER* 3.0 2.3 + - - -
673A LEU* 2.9 47.9 + - + +
693A CYS* 4.5 11.0 - - - -
697A LEU* 5.0 7.6 - - + -
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Residues in contact with VAL 670 (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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666A ALA 2.9 18.3 + - - +
667A GLN* 3.3 33.2 - - - +
669A VAL* 1.3 72.9 - - - +
671A ASP* 1.3 67.7 + - - +
673A LEU 4.5 0.2 - - - +
674A ARG* 2.8 46.2 + - - +
697A LEU* 4.2 8.7 - - + -
701A ASN* 3.2 35.9 - - + +
704A PHE* 4.0 25.6 - - + -
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Residues in contact with ASP 671 (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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667A GLN* 2.8 37.9 + - - +
668A ILE* 3.9 7.1 - - - +
670A VAL* 1.3 86.6 - - - +
672A SER* 1.3 59.9 + - - +
674A ARG* 3.2 29.8 + - - +
675A PRO* 3.3 20.4 - - - +
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Residues in contact with SER 672 (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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637A SER* 3.0 31.9 + - - +
640A PHE* 3.4 30.4 - - - +
668A ILE* 3.0 20.3 + - - +
669A VAL 3.0 2.3 + - - -
671A ASP* 1.3 79.8 - - - +
673A LEU* 1.3 59.0 + - - +
676A TYR* 3.3 27.4 - - - -
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Residues in contact with LEU 673 (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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640A PHE* 3.8 29.8 - - + -
644A SER* 4.6 1.1 - - - +
653A LEU* 4.9 0.2 - - + -
657A ILE* 4.7 1.6 - - + -
669A VAL* 2.9 36.5 + - + +
670A VAL 4.2 1.1 - - - +
672A SER* 1.3 77.0 - - - +
674A ARG* 1.3 67.3 + - - +
675A PRO* 3.3 3.1 - - - -
676A TYR* 2.7 23.1 + - + +
677A THR* 3.5 6.4 + - - -
680A LEU* 3.8 26.6 - - + +
689A VAL* 3.9 20.6 - - + -
690A ILE* 4.4 8.3 - - + -
693A CYS* 3.6 23.6 - - - -
704A PHE* 4.2 12.6 - - + -
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Residues in contact with ARG 674 (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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667A GLN* 5.2 1.6 - - - +
670A VAL* 2.8 27.9 + - - +
671A ASP* 3.2 40.7 + - - +
673A LEU* 1.3 76.3 - - - +
675A PRO* 1.3 66.1 - - + +
676A TYR 2.8 7.1 + - - -
677A THR* 3.0 22.6 + - - -
704A PHE* 3.8 30.5 - - + +
708A ALA* 5.5 1.0 - - - +
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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