Contacts of the helix formed by residues 648 - 665 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 4.0 15.7 - - + +
435A VAL* 3.7 32.5 - - + -
436A HIS* 4.2 13.0 - - + +
439A MET* 4.0 7.6 - - - +
472A LEU* 4.4 36.8 - - + +
475A ARG* 4.4 10.8 - - + -
476A LEU* 5.0 9.9 - - + +
479A THR* 4.4 11.9 - - + -
644A VAL* 2.7 26.5 + - + +
647A PHE* 1.3 75.3 - - - +
649A VAL* 1.3 64.8 + - - +
650A ASN 3.6 0.2 - - - -
651A HIS 4.4 0.2 - - - -
652A VAL* 3.0 30.2 + - + +
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Residues in contact with VAL 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TYR* 4.6 0.5 + - - -
348A ILE* 4.0 25.8 - - + +
366A ILE* 4.4 11.2 - - + -
435A VAL* 3.7 27.4 - - + -
439A MET* 3.9 13.5 - - - -
644A VAL* 3.3 9.6 + - + -
645A MET* 3.5 44.2 - - + -
648A LEU* 1.3 79.2 - - - +
650A ASN* 1.3 68.7 + - - +
652A VAL* 3.7 2.6 - - - +
653A LYS* 3.3 18.6 + - - +
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Residues in contact with ASN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A MET* 2.9 35.9 + - - +
646A HIS* 4.3 5.2 - - + +
649A VAL* 1.3 76.9 - - - +
651A HIS* 1.3 65.1 + - - +
653A LYS* 2.9 36.4 + - - +
654A ASP* 3.3 30.4 + - - +
492B ALA* 2.9 32.0 + - + +
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Residues in contact with HIS 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LEU* 5.4 0.4 - - + +
475A ARG* 3.1 59.1 + - + +
646A HIS 3.5 13.1 + - - +
647A PHE 3.3 20.4 - - - +
648A LEU 4.2 0.7 - - - +
650A ASN* 1.3 77.4 - - - +
652A VAL* 1.3 55.2 + - - +
654A ASP* 3.5 8.1 + - - +
655A THR* 2.3 63.3 + - + +
659A GLU* 5.9 1.6 - - - -
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Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TYR* 3.0 31.6 - - + +
439A MET* 4.6 0.4 - - + -
468A VAL* 5.6 2.5 - - + -
471A LEU* 3.5 28.9 - - + -
472A LEU* 3.7 21.5 - - + -
475A ARG* 4.6 11.7 - - + -
648A LEU* 3.0 25.7 + - + +
649A VAL 3.7 3.8 - - - +
650A ASN 3.3 0.2 - - - -
651A HIS* 1.3 77.2 - - - +
653A LYS* 1.3 65.6 + - - +
655A THR* 3.0 7.6 + - - -
656A LEU* 2.8 31.8 + - + +
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Residues in contact with LYS 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TYR* 4.0 10.3 - - - -
345A CYS* 3.5 41.8 - - + -
348A ILE* 3.4 25.7 - - + +
349A GLU* 2.3 49.9 + - - +
649A VAL* 3.3 5.4 + - - +
650A ASN* 2.9 35.2 + - - +
652A VAL* 1.3 80.2 - - - +
654A ASP* 1.3 68.2 + - - +
656A LEU* 4.0 4.7 + - - +
657A GLN* 4.3 5.0 + - - +
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Residues in contact with ASP 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ASN* 3.3 17.7 - - - +
651A HIS* 3.6 7.4 - - - +
652A VAL 3.2 0.4 - - - -
653A LYS* 1.3 83.6 - - - +
655A THR* 1.3 63.6 + - - +
656A LEU 3.6 0.2 + - - -
657A GLN* 3.7 15.8 + - - +
658A SER* 4.6 3.1 + - - -
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Residues in contact with THR 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LEU* 3.6 26.7 - - + -
651A HIS* 2.3 49.5 + - + -
652A VAL* 3.0 8.9 + - - -
654A ASP* 1.3 77.0 - - - +
656A LEU* 1.3 58.6 + - - +
657A GLN 3.1 1.6 + - - -
658A SER* 3.1 7.2 + - - -
659A GLU* 3.0 53.9 + - + +
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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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340A PHE* 4.5 5.2 - - + +
341A ALA* 4.1 14.2 - - + +
344A TYR* 3.3 45.8 - - + -
345A CYS* 5.9 0.4 - - - -
467A VAL* 5.8 0.4 - - + -
468A VAL* 3.4 41.3 - - + -
471A LEU* 4.0 18.6 - - + -
652A VAL* 2.8 22.6 + - + +
653A LYS 4.4 4.3 - - - +
654A ASP 3.6 0.2 - - - -
655A THR* 1.3 71.7 - - - +
657A GLN* 1.3 56.9 + - - +
658A SER 3.2 0.2 - - - -
660A LEU* 2.9 47.2 - - + +
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Residues in contact with GLN 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 5.4 0.9 - - - +
338A THR* 3.7 31.6 + - - +
341A ALA* 3.0 29.2 - - + +
342A THR* 4.1 6.6 + - - -
345A CYS* 5.5 7.7 - - - -
653A LYS 4.3 5.6 + - - +
654A ASP 3.7 14.3 + - - +
655A THR 3.1 1.0 + - - -
656A LEU* 1.3 76.9 - - - +
658A SER* 1.3 60.0 + - - +
660A LEU* 4.9 0.3 - - - +
661A VAL* 3.6 19.0 - - - +
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Residues in contact with SER 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ASP 4.9 2.8 + - - -
655A THR* 3.1 6.3 + - - -
657A GLN* 1.3 81.8 - - - +
659A GLU* 1.3 65.8 + - - +
660A LEU 2.9 1.8 - - - -
661A VAL* 3.5 8.5 - - - +
662A GLY* 2.6 28.2 + - - -
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Residues in contact with GLU 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A VAL* 4.5 2.8 - - - +
471A LEU* 4.6 10.6 - - + +
474A LYS* 3.4 29.8 + - - -
651A HIS* 5.9 1.5 - - - -
655A THR* 3.0 45.1 + - + +
658A SER* 1.3 75.4 + - - +
660A LEU* 1.3 62.8 + - - +
662A GLY* 4.3 1.8 - - - +
663A GLN* 3.3 36.4 + - + +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 3.6 36.1 - - + +
340A PHE* 4.5 16.2 - - + -
341A ALA* 4.9 3.6 - - + -
464A ILE* 3.8 22.2 - - + -
467A VAL* 3.5 28.3 - - + -
468A VAL* 4.4 6.3 - - + -
471A LEU* 5.5 1.0 - - - +
656A LEU* 2.9 41.5 + - + +
657A GLN 4.9 0.2 - - - +
658A SER 2.9 0.2 - - - -
659A GLU* 1.3 80.8 - - - +
661A VAL* 1.3 61.1 + - - +
663A GLN* 4.5 0.5 - - - +
664A LEU* 3.2 42.0 + - + +
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Residues in contact with VAL 661 (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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333A LEU 5.7 0.4 - - - +
334A LEU* 4.8 17.5 - - + -
337A ILE* 3.7 24.9 - - + -
338A THR* 4.8 7.2 - - - +
657A GLN* 3.6 20.2 - - - +
658A SER* 3.1 11.0 + - - +
660A LEU* 1.3 80.8 - - - +
662A GLY* 1.3 61.9 + - - +
664A LEU* 4.7 0.7 - - - -
665A TYR* 2.7 56.8 + - + +
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Residues in contact with GLY 662 (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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658A SER 2.6 21.3 + - - -
659A GLU* 4.3 1.3 - - - -
661A VAL* 1.3 78.9 - - - +
663A GLN* 1.3 61.9 + - - +
665A TYR* 4.2 4.7 + - - +
666A LYS* 3.3 18.0 - - - +
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Residues in contact with GLN 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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467A VAL* 4.5 22.0 + - + +
474A LYS* 5.4 5.5 - - - +
659A GLU* 3.3 30.9 + - + +
660A LEU 4.5 0.9 - - - +
662A GLY* 1.3 74.8 - - - +
664A LEU* 1.3 66.3 + - + +
666A LYS* 3.3 27.1 + - - +
669A LEU* 3.5 12.6 - - - +
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Residues in contact with LEU 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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333A LEU* 3.7 12.4 - - + +
337A ILE* 3.4 30.1 - - + -
460A LEU* 5.2 0.4 - - + +
463A ALA* 4.6 10.1 - - + -
464A ILE* 3.5 29.8 - - + +
467A VAL* 4.0 21.3 - - + -
660A LEU* 3.2 28.6 + - + +
663A GLN* 1.3 78.7 - - + +
665A TYR* 1.3 54.7 + - - +
666A LYS 2.7 15.8 + - - +
669A LEU* 3.6 20.5 - - + +
670A LEU* 5.4 0.2 - - - +
673A LEU* 4.1 21.8 - - + +
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Residues in contact with TYR 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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330A SER* 3.6 37.8 + - - -
333A LEU* 4.2 19.9 - - + +
334A LEU* 3.9 35.6 - - + +
337A ILE* 5.9 1.3 - - + -
661A VAL* 2.7 42.2 + - + +
662A GLY* 4.6 3.1 - - - +
663A GLN 3.8 0.4 - - - -
664A LEU* 1.3 68.4 - - - +
666A LYS* 1.3 65.5 + - - +
667A SER 4.4 0.2 - - - -
670A LEU* 5.2 5.2 - - + -
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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
------------------------------------------------------------
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