Contacts of the strand formed by residues 442 - 447 (chain C) in PDB entry 1XFV
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 TYR 442 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C TRP* 4.4 5.6 - + - -
367C ASP* 3.8 7.8 + - - -
369C ASP* 2.5 48.8 + - - +
370C LEU* 3.5 30.5 - - + -
374C HIS* 4.6 0.9 - + - -
439C ASN* 3.6 11.1 + - - +
441C VAL* 1.3 107.4 - - + +
443C GLU* 1.3 56.9 + - - +
444C PHE* 3.4 24.1 - + + -
455C TYR* 3.6 18.6 - + + -
456C LYS 3.3 16.2 - - - +
457C THR* 3.9 20.0 - - + +
458C LYS* 2.4 25.8 + - - -
463C THR* 3.6 14.5 + - - +
469C PHE* 4.5 6.9 - + - -
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Residues in contact with GLU 443 (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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434C LEU* 5.4 9.7 - - + +
442C TYR* 1.3 72.2 - - - +
444C PHE* 1.3 64.6 + - - +
455C TYR* 2.9 27.4 - - - +
456C LYS* 3.1 30.2 + - + +
458C LYS* 2.9 62.0 - - + +
459C GLU* 4.0 5.9 + - - +
471C TRP* 3.4 18.4 - - + -
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Residues in contact with PHE 444 (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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357C TRP* 3.4 36.1 - + - -
359C PRO* 3.1 42.0 - - + -
360C VAL* 4.6 2.0 - - + -
370C LEU* 3.7 19.3 - - + -
434C LEU* 3.5 9.8 - - - +
435C LEU* 2.7 38.8 + - + +
436C GLU 6.1 0.4 - - - -
437C SER* 5.4 10.3 - - - -
439C ASN* 5.2 2.7 - - + -
442C TYR* 3.4 29.8 - + + -
443C GLU* 1.3 81.1 - - - +
445C ARG* 1.3 65.3 + - - +
453C VAL* 5.0 2.0 - - + -
454C GLN 3.1 7.0 - - - +
455C TYR* 4.3 2.7 - - + -
471C TRP* 3.9 2.3 - - - -
474C ILE* 3.8 16.2 - - + -
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Residues in contact with ARG 445 (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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427C ASP* 3.5 23.6 + - - +
432C TYR* 2.9 42.1 + - + +
433C TYR 4.0 1.6 - - - +
434C LEU* 4.0 17.0 - - + +
435C LEU* 3.5 12.9 - - - +
444C PHE* 1.3 79.3 - - - +
446C ILE* 1.3 62.0 + - - +
447C SER 4.3 0.3 + - - -
453C VAL* 3.5 2.8 - - - +
454C GLN* 2.8 57.5 + - + +
471C TRP* 3.1 75.7 - - + +
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Residues in contact with ILE 446 (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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405C LEU* 4.1 16.4 - - + +
410C ILE* 5.3 8.3 - - + -
421C LYS* 5.5 3.8 - - - -
432C TYR* 3.7 3.8 - - - -
433C TYR* 3.0 41.9 + - + +
435C LEU* 3.1 38.4 - - + -
445C ARG* 1.3 75.2 - - - +
447C SER* 1.3 72.9 + - - +
451C ASN* 3.4 29.8 - - + +
452C GLU 3.0 17.0 - - - +
453C VAL* 4.5 8.5 - - + -
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Residues in contact with SER 447 (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 LYS* 6.1 0.7 - - - +
431C LYS 3.7 8.5 + - - -
432C TYR* 4.0 24.1 - - - -
433C TYR* 4.7 4.0 - - - -
445C ARG 4.3 0.2 + - - -
446C ILE* 1.3 88.9 - - - +
448C ASP* 1.3 68.6 + - - +
449C GLU* 3.5 3.8 + - - +
450C ASN* 2.0 42.7 + - - -
451C ASN* 3.7 5.2 - - - +
452C GLU* 2.9 21.1 + - - -
454C GLN* 5.7 3.4 + - - +
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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