Contacts of the helix formed by residues 424 - 435 (chain C) in PDB entry 2IY1
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 THR 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C GLU* 4.4 25.1 - - + +
423C ILE* 1.3 75.1 - - - +
425C GLU* 1.3 66.6 + - - +
426C GLU* 3.6 12.5 - - - +
427C MET* 2.9 36.1 + - - +
428C GLU* 2.9 22.3 + - - +
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Residues in contact with GLU 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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422C GLU* 5.5 0.2 + - - -
424C THR* 1.3 74.3 - - - +
426C GLU* 1.3 58.0 + - - +
428C GLU* 3.3 9.9 + - - +
429C LYS* 3.0 35.7 + - + +
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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 THR* 3.6 13.2 + - - +
425C GLU* 1.3 73.7 - - - +
427C MET* 1.3 74.0 + - - +
429C LYS* 3.4 11.5 + - - +
430C GLU* 3.1 35.3 + - - +
636C TRP* 4.8 6.1 + - - -
640C HIS* 5.9 1.0 + - - -
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Residues in contact with MET 427 (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 PRO 5.8 0.2 - - - +
422C GLU 3.8 9.2 - - - +
423C ILE* 3.6 31.2 - - + -
424C THR* 2.9 34.9 + - - +
426C GLU* 1.3 83.1 - - - +
428C GLU* 1.3 62.7 + - - +
430C GLU* 3.1 4.5 + - - +
431C ILE* 3.0 30.3 + - + +
633C ARG* 4.9 5.6 - - + -
636C TRP* 3.5 48.0 - - + +
644C LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ILE* 3.3 28.3 - - + +
424C THR 2.9 14.7 + - - +
425C GLU* 3.3 12.6 - - - +
427C MET* 1.3 74.6 - - - +
429C LYS* 1.3 57.0 + - + +
431C ILE* 3.2 8.9 + - - +
432C LYS* 3.0 36.5 + - - +
632C LYS* 3.7 35.3 + - - +
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Residues in contact with LYS 429 (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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425C GLU* 3.0 26.2 + - - +
426C GLU* 3.8 10.8 - - - +
427C MET 3.3 0.4 - - - -
428C GLU* 1.3 75.9 - - + +
430C GLU* 1.3 56.8 + - - +
432C LYS* 4.3 5.9 - - - +
433C ASN* 3.2 25.3 + - - +
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Residues in contact with GLU 430 (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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426C GLU* 3.1 24.9 + - - +
427C MET* 3.1 5.6 + - - +
429C LYS* 1.3 76.2 - - - +
431C ILE* 1.3 61.6 + - + +
433C ASN* 3.2 21.1 - - + +
434C VAL* 3.4 15.7 + - + +
636C TRP* 3.3 17.4 + - + -
639C LEU* 4.4 17.3 - - + +
640C HIS* 2.5 39.0 + - - -
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Residues in contact with ILE 431 (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 ILE* 4.1 18.2 - - + -
427C MET* 3.0 27.7 + - + +
428C GLU* 3.2 9.1 + - - +
430C GLU* 1.3 73.6 - - - +
432C LYS* 1.3 64.6 + - - +
433C ASN 2.9 5.2 + - - -
434C VAL* 3.0 20.8 + - - +
435C PHE* 3.1 40.8 + - + +
632C LYS* 3.5 42.0 - - + +
633C ARG* 5.2 0.2 - - - -
635C VAL* 4.2 13.7 - - + -
636C TRP* 4.3 17.7 - - + -
639C LEU* 5.6 0.4 - - + -
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Residues in contact with LYS 432 (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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428C GLU* 3.0 19.9 + - - +
429C LYS* 4.3 5.8 - - - +
431C ILE* 1.3 78.6 - - - +
433C ASN* 1.3 59.3 + - - +
435C PHE* 3.7 11.3 + - - +
436C ARG* 3.2 49.6 + - - +
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Residues in contact with ASN 433 (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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429C LYS 3.2 16.8 + - - +
430C GLU* 3.2 17.6 + - - +
431C ILE 2.9 0.2 - - - -
432C LYS* 1.3 80.0 - - - +
434C VAL* 1.3 64.1 - - - +
436C ARG* 3.4 26.6 + - - +
454C ARG* 3.8 12.0 + - - +
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Residues in contact with VAL 434 (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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430C GLU* 3.7 13.0 - - + +
431C ILE 3.0 14.4 + - - +
433C ASN* 1.3 83.2 - - - +
435C PHE* 1.3 62.2 + - + +
436C ARG 3.2 2.4 + - - -
444C LEU* 3.8 29.8 - - + -
454C ARG* 3.7 26.7 + - - +
457C ILE* 3.6 18.5 - - + +
458C GLN* 5.2 0.9 + - - +
635C VAL* 3.6 27.8 - - + -
639C LEU* 3.8 20.2 - - + -
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Residues in contact with PHE 435 (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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431C ILE* 3.1 36.6 + - + +
432C LYS* 3.9 10.1 - - - +
433C ASN 3.4 0.2 - - - -
434C VAL* 1.3 75.7 - - + +
436C ARG* 1.3 60.4 + - - +
437C ASN 3.8 0.3 + - - -
457C ILE* 3.6 32.8 - - + -
458C GLN* 2.9 27.5 + - - +
460C LEU 4.0 4.7 - - - -
461C ASN* 3.6 53.0 + - + +
462C HIS 5.5 0.2 - - - -
632C LYS* 4.7 16.4 - - + -
635C VAL* 3.6 27.4 - - + -
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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