Contacts of the helix formed by residues 560 - 566 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A CYS* 3.1 14.8 + - - -
557A LEU* 3.2 11.3 + - - +
559A ARG* 1.3 79.4 + - - +
561A GLU* 1.3 66.0 + - - +
562A PHE* 3.1 25.8 + - - -
563A LEU* 3.2 33.2 + - - +
564A LEU* 4.2 1.9 + - - +
625A VAL* 3.1 31.8 + - - +
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Residues in contact with GLU 561 (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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557A LEU 2.8 21.8 - - - +
558A GLU* 3.3 15.9 - - - +
559A ARG* 3.9 2.4 - - - -
560A SER* 1.3 77.9 + - - +
562A PHE* 1.3 54.5 + - - +
563A LEU 3.0 0.7 + - - -
564A LEU* 3.1 11.0 + - + +
565A GLU* 2.8 60.6 + - + +
414F TYR* 5.7 4.5 - - + -
416F ILE* 6.3 3.1 - - + -
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Residues in contact with PHE 562 (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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386A GLU* 3.1 39.3 - - + +
389A ALA* 4.2 3.1 - - + -
559A ARG 4.5 4.0 - - - -
560A SER* 3.6 18.8 - - - -
561A GLU* 1.3 78.6 - - - +
563A LEU* 1.3 97.0 + - + +
564A LEU 3.5 0.2 - - - -
565A GLU* 4.0 8.5 + - - -
566A LYS* 3.2 26.8 + - + +
568A ILE* 3.2 13.3 - - - +
625A VAL* 3.4 28.5 - - + -
626A LEU* 3.5 31.4 - - + -
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Residues in contact with LEU 563 (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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386A GLU 3.6 23.8 - - - +
390A GLY* 3.6 18.8 - - - +
393A TRP* 4.4 13.7 - - + -
556A CYS* 5.3 0.2 - - - -
557A LEU* 3.7 24.2 - - + -
560A SER* 3.2 20.4 + - - +
561A GLU 3.0 0.6 - - - -
562A PHE* 1.3 97.5 - - + +
564A LEU* 1.3 60.9 + - - +
567A ARG 3.4 0.7 + - - -
568A ILE* 2.8 39.8 + - + -
569A ILE* 3.5 21.9 + - + +
570A GLN* 3.5 5.9 - - - +
625A VAL* 4.3 9.9 - - + -
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Residues in contact with LEU 564 (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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557A LEU* 4.1 41.5 - - + +
560A SER 5.0 1.1 - - - +
561A GLU* 3.1 11.7 + - + +
563A LEU* 1.3 76.7 - - - +
565A GLU* 1.3 65.9 + - + +
567A ARG* 3.7 16.8 + - - -
569A ILE* 3.5 26.5 - - + -
570A GLN* 4.6 8.5 - - - +
415F ASN 4.1 9.0 - - - +
416F ILE* 4.1 35.8 - - + -
417F PRO* 4.2 9.4 - - + +
419F LYS* 5.1 11.9 - - + -
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Residues in contact with GLU 565 (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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561A GLU* 2.8 44.8 + - + +
562A PHE* 4.3 5.0 + - - -
564A LEU* 1.3 77.6 - - + +
566A LYS* 1.3 62.7 + - + +
567A ARG* 3.0 16.9 + - - +
414F TYR* 3.6 60.4 + - + +
415F ASN 4.9 0.2 - - - +
416F ILE* 5.4 3.6 - - + -
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Residues in contact with LYS 566 (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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381A SER 4.2 16.8 + - - +
382A ALA* 5.9 1.6 - - - -
383A ASP* 4.6 7.8 - - - +
386A GLU* 2.7 39.3 + - - +
387A TRP* 4.3 15.5 - - + +
562A PHE* 3.2 18.7 + - + +
565A GLU* 1.3 81.7 - - + +
567A ARG* 1.3 73.4 + - - +
568A ILE* 3.7 10.8 - - + +
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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