Contacts of the helix formed by residues 560 - 566 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556F CYS* 3.1 15.3 + - - -
557F LEU* 3.2 12.0 + - - +
559F ARG* 1.3 79.2 + - - +
561F GLU* 1.3 67.9 + - - +
562F PHE* 3.1 25.3 + - - -
563F LEU* 3.2 32.6 + - - +
564F LEU* 4.2 1.4 + - - +
625F VAL* 3.1 31.2 + - - +
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Residues in contact with GLU 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E TYR* 5.8 2.9 - - + -
416E ILE* 5.9 6.1 - - + -
557F LEU 2.8 21.8 - - - +
558F GLU 3.3 15.8 - - - +
559F ARG* 3.9 2.8 - - - -
560F SER* 1.3 79.1 + - - +
562F PHE* 1.3 55.0 + - - +
563F LEU 3.0 0.7 + - - -
564F LEU* 3.1 11.3 + - + +
565F GLU* 2.8 60.4 + - + +
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Residues in contact with PHE 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F GLU* 3.1 39.9 - - + +
389F ALA* 4.2 3.1 - - + -
559F ARG 4.5 4.5 - - - -
560F SER* 3.6 18.8 - - - -
561F GLU* 1.3 78.2 - - - +
563F LEU* 1.3 98.5 + - + +
565F GLU* 4.0 9.8 + - - -
566F LYS* 3.2 26.9 + - + +
568F ILE* 3.2 12.8 - - - +
625F VAL* 3.4 28.9 - - + -
626F LEU* 3.5 33.0 - - + -
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Residues in contact with LEU 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F GLU 3.6 15.9 - - - +
390F GLY* 3.6 27.1 - - - +
393F TRP* 4.4 13.9 - - + -
556F CYS* 5.3 0.2 - - - -
557F LEU* 3.6 23.6 - - + -
560F SER* 3.6 20.0 - - - +
561F GLU 3.0 1.0 - - - -
562F PHE* 1.3 96.4 - - + +
564F LEU* 1.3 61.3 + - - +
567F ARG 3.4 0.5 + - - -
568F ILE* 2.8 40.0 + - + -
569F ILE* 3.5 21.4 + - + +
570F GLN* 3.5 5.5 - - - +
625F VAL* 4.3 9.2 - - + -
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Residues in contact with LEU 564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E ASN 3.9 2.9 - - - +
416E ILE* 3.5 34.7 - - + -
417E PRO* 3.6 26.9 - - + +
419E LYS* 4.4 17.3 - - + -
557F LEU* 4.1 40.4 - - + +
560F SER 5.0 1.8 - - - +
561F GLU* 3.1 10.8 + - + +
563F LEU* 1.3 76.8 - - - +
565F GLU* 1.3 66.5 + - - +
567F ARG* 3.7 7.2 + - - -
569F ILE* 3.5 27.1 - - + -
570F GLN* 4.7 8.1 - - - +
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Residues in contact with GLU 565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E TYR* 3.3 65.7 - - + +
415E ASN 4.4 1.0 - - - +
416E ILE* 4.9 7.0 - - + -
561F GLU* 2.8 43.5 + - + +
562F PHE* 4.3 5.0 + - - -
564F LEU* 1.3 76.7 - - - +
566F LYS* 1.3 63.4 + - + +
567F ARG* 3.0 16.2 + - - +
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Residues in contact with LYS 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F SER 4.2 16.8 + - - +
382F ALA* 5.9 1.6 - - - -
383F ASP* 4.6 8.2 - - - +
386F GLU* 2.7 39.0 + - - +
387F TRP* 4.3 15.0 - - + +
562F PHE* 3.2 19.1 + - - +
565F GLU* 1.3 80.4 - - + +
567F ARG* 1.3 73.9 + - - +
568F ILE* 3.7 10.5 - - + +
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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