Contacts of the helix formed by residues 648 - 660 (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 HIS 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A MET 3.3 6.8 - - - +
609A THR 3.7 12.1 - - - -
610A ASP 3.5 8.7 - - - +
611A SER* 3.6 33.5 + - - -
614A ASN* 3.5 24.7 + - - +
615A TYR* 5.5 0.4 - - - -
646A ASN* 2.6 24.7 + - - +
647A PRO* 1.3 84.5 - - + +
649A GLY* 1.3 56.9 + - - +
650A THR 3.1 1.6 - - - -
651A ARG* 2.7 49.9 + - - +
652A ALA* 2.9 10.7 + - - +
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Residues in contact with GLY 649 (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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608A MET 3.0 17.4 + - - -
609A THR* 4.1 2.7 - - - -
643A ILE* 3.0 39.9 - - - +
646A ASN* 2.7 16.0 + - - -
648A HIS* 1.3 70.4 - - - +
650A THR* 1.3 55.4 + - - +
652A ALA* 3.3 1.2 + - - +
653A LEU* 2.8 26.9 + - - +
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Residues in contact with THR 650 (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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643A ILE 3.0 3.8 + - - -
644A SER* 3.7 8.1 - - - +
646A ASN 2.9 17.1 + - - +
647A PRO* 3.1 26.5 - - + +
649A GLY* 1.3 75.5 - - - +
651A ARG* 1.3 60.8 + - + +
654A GLN* 2.8 50.6 + - - +
685A ASN* 2.7 38.2 + - + +
688A HIS* 4.1 2.6 - - + +
689A VAL* 3.6 17.3 - - - +
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Residues in contact with ARG 651 (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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614A ASN* 3.0 30.9 + - - +
615A TYR* 3.3 30.2 + - - -
618A GLN* 3.8 16.7 - - - +
647A PRO* 3.6 18.8 + - - +
648A HIS* 2.7 36.1 + - - +
650A THR* 1.3 77.0 - - + +
652A ALA* 1.3 63.7 + - - +
654A GLN* 3.4 16.3 + - - +
655A LYS* 3.2 21.3 + - - +
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Residues in contact with ALA 652 (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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608A MET* 3.8 38.8 - - + +
614A ASN* 4.2 15.5 - - + +
617A ILE* 5.0 3.4 - - + -
618A GLN* 3.8 13.8 - - + +
621A LEU* 3.8 5.5 - - - +
648A HIS 2.9 10.8 + - - +
649A GLY 3.7 6.1 - - - +
651A ARG* 1.3 76.5 - - - +
653A LEU* 1.3 57.3 + - - +
655A LYS* 3.3 4.7 + - - +
656A LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 653 (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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608A MET* 5.0 4.5 - - + +
640A PHE* 3.7 56.3 - - + +
643A ILE* 4.1 11.4 - - + -
644A SER* 3.2 28.0 - - - +
649A GLY 2.8 16.4 + - - +
652A ALA* 1.3 75.3 - - - +
654A GLN* 1.3 65.8 + - - +
656A LEU* 3.5 17.4 + - + -
657A ILE* 3.2 26.7 + - + +
673A LEU* 6.0 0.2 - - + -
689A VAL* 3.8 22.4 - - + -
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Residues in contact with GLN 654 (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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650A THR* 2.8 44.8 + - - +
651A ARG* 3.7 15.7 - - - +
653A LEU* 1.3 77.4 - - - +
655A LYS* 1.3 57.8 + - - +
657A ILE* 3.3 4.9 + - - +
658A GLU* 2.9 33.6 + - - +
688A HIS* 3.3 37.0 - - - +
689A VAL* 4.2 8.5 - - - -
692A LYS* 3.6 31.0 + - + +
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Residues in contact with LYS 655 (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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618A GLN* 3.8 42.6 + - + +
621A LEU* 4.4 2.0 - - + -
622A GLU* 2.8 35.4 + - - -
651A ARG 3.2 11.6 + - - +
652A ALA 3.5 9.2 - - - +
653A LEU 3.3 0.2 - - - -
654A GLN* 1.3 76.8 - - - +
656A LEU* 1.3 66.0 - - - +
658A GLU* 3.1 26.0 + - - +
659A CYS* 2.9 36.4 + - - -
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Residues in contact with LEU 656 (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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608A MET* 3.8 25.4 - - + -
621A LEU* 3.8 26.2 - - + +
629A ARG* 5.1 0.8 - - + -
632A LEU* 4.8 0.9 - - + +
633A THR* 4.0 30.5 - - + +
636A SER* 4.0 14.1 - - - +
640A PHE* 4.7 1.6 - - + -
652A ALA 3.1 14.1 + - - +
653A LEU* 3.6 23.1 - - + +
655A LYS* 1.3 75.6 - - - +
657A ILE* 1.3 64.9 + - - +
659A CYS* 3.0 13.4 + - - +
660A ILE* 3.2 30.0 + - + +
669A VAL* 4.1 20.6 - - + -
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Residues in contact with ILE 657 (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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653A LEU* 3.2 24.7 + - + +
654A GLN* 3.5 6.7 - - - +
655A LYS 3.2 0.2 - - - -
656A LEU* 1.3 82.1 - - + +
658A GLU* 1.3 60.7 + - - +
659A CYS 3.2 0.7 + - - -
660A ILE* 3.3 22.0 + - + +
669A VAL* 4.5 17.3 - - + -
673A LEU* 4.7 0.2 - - + -
689A VAL* 3.8 26.7 - - + +
692A LYS* 3.7 24.5 - - + +
693A CYS* 3.8 24.2 - - - -
696A ARG* 4.0 20.1 - - + +
697A LEU* 4.2 15.4 - - + +
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Residues in contact with GLU 658 (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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654A GLN* 2.9 18.0 + - - +
655A LYS* 3.1 41.7 + - + +
657A ILE* 1.3 76.4 - - - +
659A CYS* 1.3 61.0 + - - +
660A ILE 3.8 2.4 + - - +
692A LYS* 2.7 35.5 + - + -
696A ARG* 3.4 47.4 + - - +
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Residues in contact with CYS 659 (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* 3.9 29.6 - - + +
622A GLU* 4.0 20.0 - - - -
629A ARG* 3.4 30.6 + - - +
655A LYS* 2.9 27.9 + - - +
656A LEU* 3.0 7.6 + - - +
658A GLU* 1.3 81.2 - - - +
660A ILE* 1.3 63.7 + - - +
661A LYS* 3.4 9.9 + - - +
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Residues in contact with ILE 660 (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* 3.7 7.4 - - - +
633A THR* 4.6 3.4 - - - +
656A LEU* 3.2 29.8 - - + +
657A ILE* 3.3 23.6 - - + +
658A GLU 3.5 2.3 - - - +
659A CYS* 1.3 77.1 - - - +
661A LYS* 1.3 62.3 + - - +
662A THR 4.9 2.7 - - - +
665A GLU* 3.4 33.9 - - + +
666A ALA* 4.1 28.0 - - + +
669A VAL* 4.4 9.0 - - + -
697A LEU* 4.1 20.4 - - + -
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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