Contacts of the helix formed by residues 594 - 605 (chain F) in PDB entry 2CEA
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 GLY 594 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441F HIS* 3.0 12.2 + - - +
593F GLU* 1.3 76.8 - - - +
595F ASP* 1.3 61.9 + - - -
596F GLU 3.0 5.6 - - - -
597F LEU* 2.8 19.6 + - - +
598F ARG* 2.9 18.9 + - - +
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Residues in contact with ASP 595 (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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593F GLU 3.7 0.4 + - - -
594F GLY* 1.3 71.7 - - - -
596F GLU* 1.3 56.7 - - - +
598F ARG* 4.1 8.8 - - - +
599F ARG* 3.1 39.4 + - - +
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Residues in contact with GLU 596 (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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585F ILE* 6.5 0.2 - - - -
589F LYS* 3.5 32.8 + - - +
592F ILE* 4.0 8.5 - - + -
593F GLU 3.3 14.0 + - - +
594F GLY 3.0 0.2 - - - -
595F ASP* 1.3 77.0 - - - +
597F LEU* 1.3 64.1 + - - +
598F ARG 3.3 0.5 + - - -
599F ARG* 3.3 15.7 - - - +
600F ILE* 2.9 51.2 - - - +
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Residues in contact with LEU 597 (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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440F VAL* 4.3 16.4 - - + +
441F HIS 3.7 6.1 - - - +
442F ARG* 3.4 35.0 - - - +
443F ILE* 3.6 19.1 - - + +
592F ILE* 3.5 24.2 - - + +
593F GLU* 3.5 11.1 + - - -
594F GLY 2.8 11.4 + - - +
596F GLU* 1.3 75.6 - - - +
598F ARG* 1.3 67.1 + - - +
600F ILE* 4.3 6.3 - - + -
601F LEU* 2.9 44.9 + - + +
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Residues in contact with ARG 598 (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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439F PRO* 5.0 6.7 - - - +
440F VAL 4.3 12.7 + - - +
441F HIS* 4.0 29.4 + - - -
594F GLY 2.9 16.0 + - - +
595F ASP* 4.2 10.3 - - - +
596F GLU 3.2 0.2 - - - -
597F LEU* 1.3 79.1 - - - +
599F ARG* 1.3 70.0 + - - +
601F LEU* 3.0 5.0 + - - +
602F SER* 3.0 24.8 + - - +
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Residues in contact with ARG 599 (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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595F ASP* 3.1 29.2 + - - +
596F GLU* 3.3 18.8 - - - +
598F ARG* 1.3 75.7 - - - +
600F ILE* 1.3 64.8 + - - +
602F SER* 2.5 31.1 + - - -
603F GLU* 2.7 16.8 + - + +
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Residues in contact with ILE 600 (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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582F ILE* 5.2 6.7 - - + -
585F ILE* 4.3 30.5 - - + -
592F ILE* 3.6 26.7 - - + -
596F GLU* 2.9 44.6 - - - +
597F LEU* 3.7 5.2 - - + +
598F ARG 3.0 0.4 + - - -
599F ARG* 1.3 84.6 - - + +
601F LEU* 1.3 75.9 + - + +
602F SER 3.1 0.2 + - - -
603F GLU* 3.1 5.9 + - - +
604F GLU* 3.1 33.1 + - + +
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Residues in contact with LEU 601 (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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428F ALA* 5.7 5.8 - - + +
432F THR* 4.3 21.7 - - + +
440F VAL* 4.3 21.5 - - + +
443F ILE* 5.7 2.0 - - + -
582F ILE* 4.2 24.5 - - + -
597F LEU* 2.9 46.0 - - + +
598F ARG* 3.0 5.0 + - - +
600F ILE* 1.3 83.6 - - + +
602F SER* 1.3 56.8 + - - +
604F GLU* 4.4 1.6 - - - -
605F PHE* 3.0 47.1 + - + +
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Residues in contact with SER 602 (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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598F ARG* 3.0 18.7 + - - +
599F ARG* 2.5 23.3 + - - -
601F LEU* 1.3 71.1 - - - +
603F GLU* 1.3 61.9 + - - +
605F PHE 3.6 18.1 - - - +
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Residues in contact with GLU 603 (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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599F ARG 2.7 14.3 + - - +
600F ILE* 3.8 8.2 - - - +
602F SER* 1.3 74.5 - - - +
604F GLU* 1.3 66.2 + - + +
605F PHE 4.5 2.6 - - - +
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Residues in contact with GLU 604 (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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575F TYR* 5.8 0.2 - - - -
577F LYS* 5.1 3.3 - - - +
578F GLN* 3.2 41.8 - - + +
581F ASN* 2.7 48.5 + - - +
582F ILE* 4.3 7.6 + - + +
585F ILE* 5.2 3.8 - - - +
600F ILE* 3.1 25.9 + - + +
601F LEU* 3.9 1.6 - - - +
603F GLU* 1.3 83.8 - - + +
605F PHE* 1.3 77.6 + - + +
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Residues in contact with PHE 605 (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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429F VAL* 4.2 23.3 - - + -
432F THR* 4.4 24.7 - - + -
433F VAL* 3.5 31.0 - - + -
575F TYR* 3.9 26.0 - + - -
578F GLN* 4.0 16.4 - - + -
582F ILE* 4.7 9.4 - - + -
601F LEU* 3.0 35.1 + - + +
602F SER* 3.6 16.3 - - - +
603F GLU 3.4 2.5 - - - +
604F GLU* 1.3 95.1 - - + +
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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