Contacts of the helix formed by residues 560 - 566 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556L CYS 3.1 14.7 + - - -
557L LEU* 3.2 12.1 + - - +
559L ARG* 1.3 78.5 + - - +
561L GLU* 1.3 67.7 + - - +
562L PHE* 3.1 25.8 + - - -
563L LEU* 3.2 32.6 + - - +
564L LEU* 4.2 1.6 + - - +
625L VAL* 3.0 32.3 + - - +
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Residues in contact with GLU 561 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K TYR* 5.7 4.0 - - + -
416K ILE* 6.2 3.8 - - + -
557L LEU 2.8 21.4 - - - +
558L GLU* 3.3 15.3 - - - +
559L ARG* 3.9 2.8 - - - -
560L SER* 1.3 79.5 + - - +
562L PHE* 1.3 54.0 + - - +
563L LEU 3.0 0.3 + - - -
564L LEU* 3.1 10.4 + - + +
565L GLU* 2.8 60.8 + - + +
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Residues in contact with PHE 562 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386L GLU* 3.1 39.0 - - + +
389L ALA* 4.2 3.6 - - + -
559L ARG 4.4 4.3 - - - -
560L SER* 3.6 17.9 - - - -
561L GLU* 1.3 77.9 - - - +
563L LEU* 1.3 98.4 + - + +
564L LEU 3.5 0.2 - - - -
565L GLU* 4.0 9.8 + - - -
566L LYS* 3.2 26.2 + - + +
568L ILE* 3.2 13.2 - - - +
625L VAL* 3.4 28.0 - - + -
626L LEU* 3.5 31.6 - - + -
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Residues in contact with LEU 563 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386L GLU 3.6 16.6 - - - +
390L GLY* 3.6 27.1 - - - +
393L TRP* 4.4 13.0 - - + -
556L CYS* 5.3 0.2 - - - -
557L LEU* 3.6 24.2 - - + -
560L SER* 3.6 20.0 - - - +
561L GLU 3.0 1.0 - - - -
562L PHE* 1.3 96.0 - - + +
564L LEU* 1.3 62.2 + - - +
567L ARG 3.4 0.7 + - - -
568L ILE* 2.8 39.7 + - + -
569L ILE* 3.5 20.7 + - + +
570L GLN* 3.5 5.9 - - - +
625L VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 564 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K ASN 4.0 9.0 - - - +
416K ILE* 3.9 38.5 - - + -
417K PRO* 4.1 8.5 - - + +
419K LYS* 4.9 13.7 - - + -
557L LEU* 4.1 40.2 - - + +
560L SER 5.0 2.0 - - - +
561L GLU* 3.1 11.0 + - + +
563L LEU* 1.3 74.8 - - - +
565L GLU* 1.3 67.4 + - + +
567L ARG* 3.7 16.0 + - - -
569L ILE* 3.5 27.1 - - + -
570L GLN* 4.6 8.3 - - - +
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Residues in contact with GLU 565 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K TYR* 3.5 62.0 - - + +
415K ASN 4.7 0.3 - - - +
416K ILE* 5.3 4.5 - - + -
561L GLU* 2.8 43.3 + - + +
562L PHE* 4.3 4.5 + - - -
564L LEU* 1.3 77.8 - - + +
566L LYS* 1.3 62.7 + - + +
567L ARG* 3.0 16.8 + - - +
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Residues in contact with LYS 566 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381L SER 4.2 17.0 + - - +
382L ALA* 5.9 1.3 - - - -
383L ASP* 4.6 8.0 - - - +
386L GLU* 2.7 39.1 + - - +
387L TRP* 4.3 15.6 - - + +
562L PHE* 3.2 18.9 + - + +
565L GLU* 1.3 80.4 - - + +
567L ARG* 1.3 73.4 + - - +
568L ILE* 4.0 10.1 - - + +
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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