Contacts of the helix formed by residues 648 - 665 (chain B) in PDB entry 4BEJ
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 648 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 4.5 4.9 - - + +
435B VAL* 3.6 32.8 - - + -
436B HIS* 4.3 11.9 - - + +
439B MET* 3.9 9.2 - - - -
472B LEU* 3.9 33.0 - - + +
475B ARG* 4.1 18.2 - - + -
476B LEU* 4.8 13.5 - - + +
479B THR* 4.4 15.0 - - + -
644B VAL* 2.8 19.8 + - + +
646B HIS 3.6 0.2 - - - -
647B PHE* 1.3 79.8 - - - +
649B VAL* 1.3 66.5 + - - +
650B ASN 3.6 0.2 - - - -
652B VAL* 3.0 29.5 + - - +
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Residues in contact with VAL 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TYR* 4.7 0.2 + - - -
348B ILE* 4.0 29.0 - - + +
366B ILE* 4.5 7.9 - - + -
435B VAL* 4.0 25.8 - - + -
439B MET* 4.0 13.9 - - - -
644B VAL* 3.3 6.0 + - + -
645B MET* 3.6 47.6 - - + +
648B LEU* 1.3 77.4 - - - +
650B ASN* 1.3 63.4 + - - +
652B VAL* 3.3 2.9 + - - +
653B LYS* 3.1 25.3 + - - +
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Residues in contact with ASN 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ALA* 3.1 31.2 + - + +
645B MET* 2.7 35.3 + - - +
646B HIS* 4.2 5.4 - - + +
649B VAL* 1.3 76.4 - - - +
651B HIS* 1.3 64.4 + - - +
653B LYS* 3.2 32.7 + - - +
654B ASP* 3.2 33.7 + - - +
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Residues in contact with HIS 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B LEU* 5.6 3.3 - - + +
475B ARG* 3.1 59.9 + - + +
646B HIS 3.5 9.1 + - - +
647B PHE 3.2 23.6 - - - +
648B LEU 4.0 0.7 - - - +
650B ASN* 1.3 78.4 - - - +
652B VAL* 1.3 54.1 + - - +
654B ASP* 3.5 7.1 + - - +
655B THR* 2.6 60.1 + - + +
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Residues in contact with VAL 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TYR* 3.0 33.7 - - + +
439B MET* 4.5 1.3 - - + -
468B VAL* 5.7 2.5 - - + -
471B LEU* 4.5 12.6 - - + -
472B LEU* 3.6 28.7 - - + -
475B ARG* 4.5 14.6 - - + -
648B LEU* 3.0 26.3 + - + +
649B VAL 3.6 3.4 - - - +
651B HIS* 1.3 76.5 - - - +
653B LYS* 1.3 65.7 + - - +
655B THR* 2.6 21.0 + - - +
656B LEU* 3.0 23.0 + - + +
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Residues in contact with LYS 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TYR* 4.2 9.4 - - - -
345B CYS* 3.6 36.6 - - + -
348B ILE* 3.4 28.4 - - + +
349B GLU* 3.5 39.3 + - - +
649B VAL* 3.1 9.0 + - - +
650B ASN* 3.2 31.9 + - - +
652B VAL* 1.3 78.1 - - - +
654B ASP* 1.3 68.9 + - - +
656B LEU* 4.6 1.0 - - - +
657B GLN* 4.0 10.9 + - - +
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Residues in contact with ASP 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B ASN* 3.2 19.9 + - - +
651B HIS* 3.7 7.9 - - - +
653B LYS* 1.3 81.5 - - - +
655B THR* 1.3 58.5 + - + +
657B GLN* 3.0 44.4 + - - +
658B SER* 4.3 1.6 + - - -
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Residues in contact with THR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B LEU* 4.0 11.8 - - + +
651B HIS* 2.6 44.8 + - + +
652B VAL* 2.6 28.6 + - - -
654B ASP* 1.3 72.2 - - + +
656B LEU* 1.3 49.4 + - - +
657B GLN 3.1 4.3 - - - -
658B SER* 2.8 16.2 + - - -
659B GLU* 2.7 53.4 + - + +
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Residues in contact with LEU 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE* 5.0 4.5 - - + +
341B ALA* 4.9 5.8 - - - -
344B TYR* 3.2 44.9 - - + -
345B CYS* 6.1 0.4 - - - -
467B VAL* 5.4 1.1 - - + -
468B VAL* 3.4 39.3 - - + -
471B LEU* 3.9 23.3 - - + +
652B VAL* 3.0 18.0 + - + +
653B LYS 4.6 1.8 - - - +
655B THR* 1.3 72.8 + - - +
657B GLN* 1.3 63.4 + - - +
658B SER 3.1 0.4 - - - -
659B GLU* 4.1 3.4 - - - +
660B LEU* 3.1 54.4 - - + +
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Residues in contact with GLN 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 6.0 1.4 - - - +
341B ALA* 4.1 21.9 - - + +
345B CYS* 5.1 9.7 - - - -
653B LYS 4.0 11.1 + - - +
654B ASP* 3.0 29.6 + - - +
655B THR 3.0 0.2 + - - -
656B LEU* 1.3 77.8 - - - +
658B SER* 1.3 66.0 + - - +
660B LEU* 5.1 0.7 - - - +
661B VAL* 3.3 15.5 - - - +
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Residues in contact with SER 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B ASP 4.3 1.7 + - - -
655B THR* 2.8 13.6 + - - -
657B GLN* 1.3 90.6 + - - +
659B GLU* 1.3 62.1 + - - +
660B LEU 3.0 2.2 + - - -
661B VAL* 3.2 10.3 + - - +
662B GLY* 2.8 25.3 + - - -
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Residues in contact with GLU 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 5.2 2.2 - - + -
471B LEU* 3.5 28.4 - - + +
474B LYS* 3.7 11.4 + - - -
655B THR* 2.7 42.1 + - + +
656B LEU* 5.0 2.2 - - - +
658B SER* 1.3 74.5 + - - +
660B LEU* 1.3 62.3 + - - +
662B GLY* 3.8 2.7 - - - +
663B GLN* 3.2 36.9 + - + +
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Residues in contact with LEU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE* 4.3 25.4 - - + +
340B PHE* 4.1 20.6 - - + -
341B ALA* 4.7 7.0 - - + +
464B ILE* 3.7 28.5 - - + -
467B VAL* 3.6 26.9 - - + -
468B VAL* 4.0 2.5 - - + -
656B LEU* 3.1 52.9 + - + +
657B GLN 5.1 0.4 - - - +
658B SER 3.0 0.6 - - - -
659B GLU* 1.3 77.6 - - - +
661B VAL* 1.3 68.0 + - + +
664B LEU* 3.2 31.2 + - + +
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Residues in contact with VAL 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.9 11.7 - - + -
337B ILE* 3.6 23.1 - - + +
338B THR* 5.8 3.1 - - - +
657B GLN 3.3 23.3 - - - +
658B SER* 3.3 17.9 - - - +
660B LEU* 1.3 74.7 - - + +
662B GLY* 1.3 61.6 + - - +
665B TYR* 2.7 52.8 + - + +
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Residues in contact with GLY 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B SER 2.8 15.7 + - - -
659B GLU* 4.1 2.2 - - - -
660B LEU 3.3 0.2 - - - -
661B VAL* 1.3 83.7 - - - +
663B GLN* 1.3 61.7 + - - +
665B TYR* 4.2 4.2 + - - +
666B LYS* 4.3 13.3 - - - +
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Residues in contact with GLN 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B GLU* 5.9 0.2 + - - -
467B VAL* 3.4 32.4 - - + +
474B LYS* 4.8 12.1 + - - -
659B GLU* 3.2 24.5 + - + +
662B GLY* 1.3 76.5 - - - +
664B LEU* 1.4 69.4 + - + +
666B LYS* 3.7 21.7 - - - +
669B LEU* 5.5 4.7 - - - +
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Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LEU* 3.7 17.0 - - + +
337B ILE* 4.4 15.0 - - + -
460B LEU* 4.9 1.6 - - + +
463B ALA* 4.1 21.5 - - + -
464B ILE* 4.2 20.4 - - + -
467B VAL* 3.8 31.6 - - + -
660B LEU* 3.2 24.1 + - + +
661B VAL 4.2 0.2 - - - +
663B GLN* 1.4 76.6 - - + +
665B TYR* 1.3 55.5 + - - +
666B LYS* 2.7 19.0 + - - +
669B LEU* 4.8 9.4 - - + +
673B LEU* 3.4 34.7 - - + +
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Residues in contact with TYR 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER* 3.8 32.3 + - - -
333B LEU* 4.4 17.5 - - + -
334B LEU* 3.9 35.6 - - + +
337B ILE* 5.1 1.5 - - + +
661B VAL* 2.7 40.9 + - + +
662B GLY* 4.6 2.2 - - - +
664B LEU* 1.3 69.9 - - - +
666B LYS* 1.3 65.6 + - - +
670B LEU* 4.6 4.0 - - + -
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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
------------------------------------------------------------
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