Contacts of the helix formed by residues 560 - 566 (chain E) in PDB entry 4E2I
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 SER 560 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556E CYS* 3.1 15.3 + - - -
557E LEU* 3.2 11.8 + - - +
559E ARG* 1.3 79.1 + - - +
561E GLU* 1.3 66.5 + - - +
562E PHE* 3.1 25.8 + - - -
563E LEU* 3.2 32.6 + - - +
564E LEU* 4.2 1.4 + - - +
625E VAL* 3.1 31.9 + - - +
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Residues in contact with GLU 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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414D TYR* 5.8 4.0 - - + -
416D ILE* 6.4 1.8 - - + -
557E LEU 2.8 21.0 - - - +
558E GLU* 3.3 15.5 - - - +
559E ARG* 3.9 3.4 - - - -
560E SER* 1.3 78.3 + - - +
562E PHE* 1.3 53.9 + - - +
563E LEU 3.1 0.7 + - - -
564E LEU* 3.1 11.4 + - + +
565E GLU* 2.8 60.7 + - + +
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Residues in contact with PHE 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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386E GLU* 3.1 41.1 - - + +
389E ALA* 4.2 3.6 - - + -
559E ARG 4.5 5.2 - - - -
560E SER* 3.6 17.0 - - - -
561E GLU* 1.3 77.4 - - - +
563E LEU* 1.3 97.2 + - + +
564E LEU 3.5 0.2 - - - -
565E GLU* 4.0 9.4 + - - -
566E LYS* 3.2 25.7 + - + +
568E ILE* 3.2 13.3 - - - +
625E VAL* 3.4 28.5 - - + -
626E LEU* 3.5 31.0 - - + -
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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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386E GLU 3.6 15.9 - - - +
390E GLY* 3.6 26.9 - - - +
393E TRP* 4.4 13.2 - - + -
557E LEU* 3.6 23.8 - - + -
560E SER* 3.2 20.4 + - - +
561E GLU 3.0 0.8 - - - -
562E PHE* 1.3 96.4 - - + +
564E LEU* 1.3 63.1 + - - +
567E ARG 3.4 0.9 + - - -
568E ILE* 2.8 39.9 + - + -
569E ILE* 3.5 21.2 + - + +
570E GLN* 3.5 5.4 - - - +
625E VAL* 4.2 9.9 - - + -
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Residues in contact with LEU 564 (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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415D ASN 4.2 6.8 - - - +
416D ILE* 4.2 36.3 - - + -
417D PRO* 4.3 7.3 - - + +
419D LYS* 5.2 11.2 - - + -
557E LEU* 4.1 40.4 - - + +
560E SER 5.0 1.6 - - - +
561E GLU* 3.1 12.1 + - + +
563E LEU* 1.3 76.3 - - - +
565E GLU* 1.3 66.9 + - + +
567E ARG* 3.7 19.1 + - - -
569E ILE* 3.5 27.6 - - + -
570E GLN* 4.6 8.7 - - - +
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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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414D TYR* 3.6 59.2 + - + +
415D ASN 5.0 0.2 - - - +
416D ILE* 5.5 4.9 - - + -
561E GLU* 2.8 43.3 + - + +
562E PHE* 4.3 4.8 + - - -
564E LEU* 1.3 77.2 - - + +
566E LYS* 1.3 63.0 + - + +
567E ARG* 3.0 15.7 + - - +
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Residues in contact with LYS 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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381E SER 4.2 17.2 + - - +
382E ALA* 5.9 1.6 - - - -
383E ASP* 4.6 8.0 - - - +
386E GLU* 2.7 39.1 + - - +
387E TRP* 4.3 15.8 - - + +
562E PHE* 3.2 20.0 + - + +
565E GLU* 1.3 81.9 - - + +
567E ARG* 1.3 73.3 + - - +
568E ILE* 3.7 10.4 - - + +
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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