Contacts of the strand formed by residues 450 - 456 (chain C) in PDB entry 3WF4
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 ILE 450 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446C ALA* 3.3 1.9 - - - -
447C VAL 2.8 37.5 + - - +
448C ASP* 3.8 6.7 - - + +
449C GLY* 1.3 78.3 - - - +
451C PRO* 1.3 73.4 - - + +
452C GLN* 2.8 34.4 + - - +
466C THR 5.9 0.7 - - - +
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Residues in contact with PRO 451 (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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445C VAL 3.6 7.4 - - - +
446C ALA* 4.3 3.1 - - + -
449C GLY 3.3 11.6 - - - +
450C ILE* 1.3 95.3 - - + +
452C GLN* 1.3 63.0 + - - +
453C GLY 4.9 0.2 - - - +
546C TYR* 3.7 42.5 - - + +
547C THR* 3.7 21.1 - - - +
548C LEU* 3.8 10.7 - - + +
549C PRO* 6.2 0.7 - - + -
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Residues in contact with GLN 452 (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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445C VAL* 2.7 24.7 + - + +
446C ALA 4.2 0.9 - - - -
447C VAL* 3.6 34.9 - - + +
450C ILE* 2.8 41.7 + - - +
451C PRO* 1.3 72.9 + - - +
453C GLY* 1.3 55.6 + - - +
463C LEU* 3.8 14.5 - - + +
464C ASN 4.1 5.6 - - - +
465C ILE* 3.2 24.3 - - + -
466C THR* 3.2 33.0 + - - +
546C TYR* 4.6 4.8 - - - -
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Residues in contact with GLY 453 (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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445C VAL* 3.0 29.4 + - - +
451C PRO* 3.7 1.6 - - - +
452C GLN* 1.3 79.9 - - - +
454C VAL* 1.3 65.0 + - - +
463C LEU* 3.9 7.6 - - - -
546C TYR* 3.5 33.3 - - - -
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Residues in contact with VAL 454 (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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442C ARG* 3.7 28.3 - - + +
443C ALA 3.4 8.7 - - - +
444C TYR* 3.8 22.2 - - + -
453C GLY* 1.3 79.5 - - - +
455C LEU* 1.3 73.5 + - - +
456C GLU* 3.8 16.2 - - + +
460C VAL* 3.5 19.1 - - - +
463C LEU* 3.9 12.2 - - - +
546C TYR* 3.7 29.3 + - + +
622C GLU* 4.1 9.2 - - + -
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Residues in contact with LEU 455 (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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432C LEU* 4.1 14.1 - - + +
434C SER 5.4 0.2 - - - +
439C VAL* 4.0 29.2 - - + +
442C ARG* 3.5 4.2 - - - -
443C ALA* 3.0 29.8 + - + +
445C VAL* 4.5 5.0 - - + +
454C VAL* 1.3 75.6 - - - +
456C GLU* 1.3 60.0 + - - +
460C VAL* 3.5 5.2 - - + +
461C ILE* 3.8 31.0 - - - +
462C THR 3.9 1.6 - - - -
463C LEU* 3.6 33.4 - - + +
475C LEU* 3.8 28.9 - - + -
499C LEU* 4.5 10.3 - - + -
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Residues in contact with GLU 456 (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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437C ASN* 4.5 0.4 + - - -
439C VAL* 4.7 3.4 - - - -
441C ASP 4.1 3.6 - - - +
442C ARG* 3.3 38.1 + - + +
454C VAL* 3.8 13.9 - - + +
455C LEU* 1.3 77.5 - - - +
457C ARG* 1.3 64.7 - - - +
458C ASN 3.2 2.1 + - - -
459C ASN* 3.0 30.6 + - - +
460C VAL* 2.8 52.8 + - + +
461C ILE* 4.3 2.8 - - - +
595C ARG* 4.0 9.9 + - - -
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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