Contacts of the helix formed by residues 560 - 575 (chain E) in PDB entry 4E3C
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 560 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E ILE* 4.6 6.5 - - + -
440E LEU* 3.7 13.2 - - + +
441E LYS* 3.6 35.3 - - + +
444E CYS* 4.3 10.5 - - + -
559E THR* 1.3 80.8 - - - +
561E ASP* 1.3 63.5 + - - +
563E LEU* 3.3 8.4 + - + +
564E GLU* 3.2 23.0 + - - +
597E ALA* 3.2 44.0 - - + +
600E SER* 3.7 9.8 + - - +
601E PHE* 4.1 20.0 - - + +
604E LYS* 3.8 15.5 - - + +
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Residues in contact with ASP 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E LYS* 3.6 44.7 + - - +
445E ASN* 4.6 9.0 + - - +
559E THR 3.2 6.2 + - - +
560E LEU* 1.3 78.8 - - - +
562E ASP* 1.3 61.4 + - - +
564E GLU* 3.9 0.9 + - - +
565E GLU* 3.7 16.3 + - - +
604E LYS* 4.0 21.3 + - - -
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Residues in contact with ASP 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559E THR* 3.0 20.7 + - - +
561E ASP* 1.3 78.4 - - - +
563E LEU* 1.3 59.9 + - - +
565E GLU* 3.0 9.7 + - - +
566E GLN* 2.7 56.7 + - - +
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Residues in contact with LEU 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E ILE* 4.5 12.3 - - + +
559E THR* 3.0 18.3 + - + +
560E LEU* 3.3 8.5 + - + +
562E ASP* 1.3 79.1 + - - +
564E GLU* 1.3 64.5 + - - +
566E GLN* 3.0 16.8 + - - +
567E ALA* 2.8 27.0 + - - +
593E LEU* 4.5 18.5 - - + +
596E GLN* 3.2 52.3 - - + +
597E ALA* 3.4 18.6 - - + +
600E SER* 4.4 9.4 - - - -
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Residues in contact with GLU 564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E TRP* 3.0 25.5 - - + -
437E ILE* 3.9 16.7 - - + +
438E GLN* 2.8 61.0 + - + +
441E LYS* 3.6 32.9 + - + +
560E LEU 3.2 13.0 + - - +
561E ASP 4.0 2.0 - - - +
562E ASP 3.3 0.2 - - - -
563E LEU* 1.3 79.4 - - - +
565E GLU* 1.3 63.0 + - - +
567E ALA* 3.5 2.3 + - - +
568E ARG* 2.8 29.8 + - - -
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Residues in contact with GLU 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E LYS* 6.0 0.9 - - - +
561E ASP 3.7 9.9 + - - +
562E ASP* 3.0 11.0 + - - +
564E GLU* 1.3 84.8 + - - +
566E GLN* 1.3 68.5 + - - +
568E ARG* 3.1 34.7 + - + +
569E GLU* 3.4 9.2 + - + +
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Residues in contact with GLN 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562E ASP* 2.7 38.1 + - - +
563E LEU* 3.0 13.9 + - - +
565E GLU* 1.3 72.6 - - - +
567E ALA* 1.3 63.6 + - - +
569E GLU* 3.1 24.6 - - + +
570E LEU* 3.3 9.0 - - + +
589E GLU* 5.9 1.0 + - - -
592E ARG* 4.9 4.8 - - - +
593E LEU* 3.3 31.8 - - + +
596E GLN* 5.7 0.8 + - - -
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Residues in contact with ALA 567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E TRP* 3.7 18.6 - - + -
437E ILE* 4.1 14.1 - - + -
563E LEU 2.8 15.9 + - - +
564E GLU 3.7 4.5 - - - +
566E GLN* 1.3 72.5 - - - +
568E ARG* 1.3 68.5 + - - +
569E GLU 2.9 2.2 - - - -
570E LEU* 2.8 27.6 + - - +
571E TYR* 3.1 13.3 - - + -
590E MET* 4.5 4.0 - - - -
593E LEU* 3.8 17.9 - - + +
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Residues in contact with ARG 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU* 3.6 21.8 + - - +
434E TRP* 2.8 40.3 - - + -
438E GLN* 4.2 2.8 - - - +
441E LYS* 5.5 2.0 - - - +
564E GLU* 2.8 31.7 + - - -
565E GLU* 3.1 26.2 + - - +
567E ALA* 1.3 79.5 - - - +
569E GLU* 1.3 63.5 + - - +
570E LEU 3.0 1.4 + - - -
571E TYR* 3.1 25.3 + - + +
572E ARG* 3.1 18.4 + - + +
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Residues in contact with GLU 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565E GLU* 3.4 9.4 + - + +
566E GLN* 3.1 21.4 + - + +
567E ALA 2.8 1.2 + - - -
568E ARG* 1.3 79.6 - - - +
570E LEU* 1.3 61.0 + - + +
572E ARG* 3.4 40.3 + - - +
573E ARG* 2.8 46.0 + - - +
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Residues in contact with LEU 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E TRP* 3.3 36.5 - - + -
566E GLN* 3.3 16.8 - - + +
567E ALA* 2.8 30.4 + - - +
569E GLU* 1.3 71.5 - - + +
571E TYR* 1.3 59.6 + - - +
573E ARG* 3.0 14.6 + - - +
574E LEU* 2.8 30.9 + - - +
589E GLU* 4.3 28.3 - - + +
590E MET* 3.2 26.5 - - + -
593E LEU* 4.1 9.0 - - + -
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Residues in contact with TYR 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PHE* 5.5 6.3 - - + +
427E ARG 5.0 0.4 - - - -
430E TRP* 2.6 43.8 + + + -
431E GLY* 2.9 15.9 - - - -
434E TRP* 2.8 50.1 + + + +
567E ALA 3.1 23.8 - - - -
568E ARG* 3.3 13.9 - - + +
570E LEU* 1.3 74.0 - - - +
572E ARG* 1.3 57.8 + - - +
574E LEU* 2.9 7.7 + - + +
575E ARG* 2.7 71.7 + - - +
590E MET* 3.3 21.4 - - + -
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Residues in contact with ARG 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PHE* 4.7 13.9 - - + +
112E GLU* 5.7 3.6 - - - +
568E ARG* 3.1 19.6 + - + +
569E GLU* 3.4 36.4 + - - +
571E TYR* 1.3 79.4 - - - +
573E ARG* 1.3 80.1 + - - +
576E GLU* 3.0 58.8 + - - +
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Residues in contact with ARG 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569E GLU* 2.8 61.3 + - - +
570E LEU* 3.0 13.6 + - - +
571E TYR 2.9 0.8 - - - -
572E ARG* 1.3 96.1 - - - +
574E LEU* 1.3 58.7 + - - +
576E GLU* 4.1 1.2 - - - -
577E LYS* 3.1 39.1 + - + +
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Residues in contact with LEU 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E LEU* 3.1 39.7 - - + +
427E ARG* 3.9 18.2 - - + +
430E TRP* 3.9 18.6 - - + -
570E LEU 2.8 13.5 + - - +
571E TYR* 2.9 6.1 + - + +
573E ARG* 1.3 77.6 - - - +
575E ARG* 1.3 58.4 + - - +
576E GLU 2.9 4.5 - - - -
577E LYS* 2.8 43.5 + - + +
582E ARG* 3.2 37.1 + - - +
584E GLU* 4.6 4.7 - - - +
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Residues in contact with ARG 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASN 5.5 0.4 - - - -
111E PHE* 3.0 49.9 + - + +
114E CYS* 3.7 32.0 - - - +
115E CYS* 3.9 6.1 - - - -
427E ARG* 2.9 67.8 + - + +
428E LYS* 5.1 1.8 - - - +
431E GLY* 4.0 3.0 - - - -
434E TRP* 5.6 0.6 - - - +
571E TYR* 2.7 60.8 + - - +
574E LEU* 1.3 76.7 - - - +
576E GLU* 1.3 59.0 + - - +
577E LYS 4.7 2.2 - - - +
579E ARG* 5.9 2.1 - - - +
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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