Contacts of the strand formed by residues 510 - 516 (chain X) in PDB entry 4HSC
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 PHE 510 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467X LEU* 4.5 8.5 - - + -
469X HIS* 2.9 48.4 + - + +
470X GLN* 3.7 1.4 + - - +
477X TYR* 4.1 17.3 - + - -
499X TRP* 4.0 18.6 - + - -
501X ASN* 5.8 0.4 - - - -
506X LYS* 3.7 44.0 - - + -
507X THR 3.3 14.8 - - - +
509X PRO* 1.3 76.8 - - - +
511X SER* 1.3 78.6 + - - +
512X THR* 3.7 26.7 - - - -
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Residues in contact with SER 511 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467X LEU 3.3 14.5 + - - -
468X SER* 4.3 4.9 - - - -
470X GLN* 4.3 8.3 + - - -
510X PHE* 1.3 92.9 + - - +
512X THR* 1.3 70.1 + - - +
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Residues in contact with THR 512 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465X ILE 4.5 0.2 - - - -
466X ASN* 3.7 2.1 - - - +
467X LEU* 3.1 34.0 + - - +
499X TRP* 4.5 15.9 - - + +
510X PHE* 3.7 21.0 - - - -
511X SER* 1.3 80.7 + - - +
513X VAL* 1.3 92.6 + - - +
514X ILE* 4.5 9.6 - - + -
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Residues in contact with VAL 513 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464X LYS* 3.8 30.1 - - + -
465X ILE 3.4 3.1 - - - +
466X ASN* 3.3 26.5 - - - +
512X THR* 1.3 91.5 - - - +
514X ILE* 1.3 66.0 + - - +
515X PRO* 3.5 11.2 - - + +
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Residues in contact with ILE 514 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464X LYS* 3.4 3.9 - - - -
465X ILE* 2.8 59.6 + - + +
467X LEU* 3.8 14.4 - - + -
479X ILE* 3.6 33.9 - - + -
481X TRP* 3.9 29.2 - - + -
499X TRP* 3.6 40.8 - - + +
512X THR* 4.5 4.5 - - + -
513X VAL* 1.3 79.2 - - - +
515X PRO* 1.3 70.5 - - + +
516X LEU 3.6 0.2 + - - -
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Residues in contact with PRO 515 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463X GLY 3.8 6.5 - - - +
464X LYS* 4.6 7.9 - - + -
481X TRP* 4.0 10.4 - - - -
513X VAL* 3.5 11.7 - - + +
514X ILE* 1.3 88.0 - - + +
516X LEU* 1.3 68.0 + - - +
517X GLY 4.0 1.2 + - - -
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Residues in contact with LEU 516 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X SER* 3.6 4.9 - - - -
463X GLY 2.9 31.1 + - - +
465X ILE* 3.5 38.4 - - + -
481X TRP* 3.1 46.2 - - + +
514X ILE 4.2 0.7 - - - +
515X PRO* 1.3 72.8 - - - +
517X GLY* 1.3 65.3 + - - +
520X SER* 3.9 4.9 - - - +
523X ILE* 3.7 39.3 - - + -
549X LEU* 3.8 18.6 - - + -
553X ILE* 4.2 5.4 - - + -
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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