Contacts of the strand formed by residues 420 - 426 (chain C) in PDB entry 2FH2
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 LYS 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416C GLY 5.3 0.8 + - - -
418C GLY 4.6 7.4 + - - +
419C GLN* 1.3 84.5 - - - +
421C GLN* 1.3 67.1 + - - +
422C ILE* 4.6 8.5 - - + -
438C TYR* 3.5 39.8 + - + +
449C ILE* 4.7 5.2 - - + -
450C LEU 3.2 13.7 - - - +
451C TYR* 4.0 12.1 - - + -
452C ASN* 4.7 1.6 - - - -
511C LEU* 3.0 46.6 + - + +
512C PHE* 4.0 19.4 - - + +
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Residues in contact with GLN 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C GLN* 6.1 2.7 - - + +
420C LYS* 1.3 78.0 - - - +
422C ILE* 1.3 63.4 + - - +
423C TRP* 3.4 35.2 - - + -
438C TYR* 3.5 6.5 - - - +
449C ILE* 3.5 2.6 - - - +
450C LEU* 2.9 61.4 + - - +
452C ASN* 5.0 4.9 + - - -
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Residues in contact with ILE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C LYS* 4.6 6.1 - - + -
421C GLN* 1.3 79.9 - - - +
423C TRP* 1.3 72.5 + - - +
432C PRO* 3.9 3.3 - - - +
433C VAL* 3.1 28.8 + - + +
438C TYR* 3.1 55.9 + - + -
441C PHE* 4.1 23.1 - - + -
447C TYR* 4.0 17.0 - - + -
448C ILE 3.4 9.4 - - - +
449C ILE* 4.0 22.4 - - + -
512C PHE* 4.2 12.1 - - + -
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Residues in contact with TRP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C GLN* 3.4 47.6 - - + -
422C ILE* 1.3 75.3 - - - +
424C ARG* 1.3 61.6 + - - +
430C LYS* 3.5 47.8 - - + +
431C VAL 3.4 8.1 - - - +
432C PRO* 3.7 33.2 - - + +
433C VAL* 3.8 3.8 - - - -
447C TYR* 3.3 8.5 - - - -
448C ILE* 2.9 50.8 + - + +
450C LEU* 3.7 30.7 - - + -
486C LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C TRP* 1.3 74.7 - - - +
425C ILE* 1.3 69.3 + - - +
426C GLU* 3.2 38.6 + - - +
430C LYS* 3.4 1.2 - - - -
431C VAL* 2.8 34.4 + - - +
433C VAL* 3.7 9.4 - - + +
442C TYR* 3.4 21.9 - - - -
445C ASP* 2.9 29.1 + - + +
446C SER 3.7 9.2 - - - +
447C TYR* 3.7 28.5 + - + -
524C THR* 3.7 15.2 - - - +
530C GLN* 2.9 36.1 + - - +
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Residues in contact with ILE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C TRP 5.0 0.2 - - - +
424C ARG* 1.3 77.7 - - - +
426C GLU* 1.3 63.4 + - - +
427C GLY 3.7 19.2 + - - +
429C ASN 3.6 3.8 - - - +
430C LYS* 4.7 2.5 - - + -
445C ASP* 5.1 1.2 - - - +
446C SER* 3.1 29.9 + - - +
447C TYR* 4.2 2.0 - - - +
448C ILE* 3.7 29.6 - - + +
475C GLU* 3.8 38.6 - - + +
478C ALA* 4.2 4.0 - - + -
479C SER* 3.5 33.0 - - - -
482C LEU* 3.6 16.8 - - + -
524C THR* 4.1 8.8 - - - +
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Residues in contact with GLU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C ARG* 3.2 44.1 + - - +
425C ILE* 1.3 77.0 - - - +
427C GLY* 1.3 62.9 + - - +
428C SER 3.4 2.1 + - - -
429C ASN* 3.1 24.1 + - - +
431C VAL* 3.6 39.0 - - + +
432C PRO 5.4 0.3 - - - +
475C GLU* 5.9 0.2 - - - -
524C THR* 4.0 15.6 + - + +
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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