Contacts of the strand formed by residues 454 - 461 (chain C) in PDB entry 1S9K
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 LEU 454 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C LEU* 4.6 11.7 - - + -
448C TYR* 2.9 25.8 - - + +
452C LYS* 2.9 31.0 - - + +
453C PRO* 1.3 76.9 - - - +
455C GLY* 1.3 64.7 + - - +
456C LEU 4.0 0.2 - - - -
502C PRO* 3.6 6.8 - - - +
503C LEU* 3.0 30.0 + - + -
509C MET* 4.2 9.2 - - + -
548C VAL* 5.0 8.5 - - + -
549C HIS 3.9 24.2 - - - +
550C ILE* 4.1 27.8 - - + -
551C PRO* 4.6 8.5 - - + -
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Residues in contact with GLY 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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454C LEU* 1.3 78.5 - - - +
456C LEU* 1.3 63.7 + - - -
457C GLN* 3.6 6.8 + - - +
500C GLU* 4.1 20.0 - - - +
501C ILE 4.3 3.4 - - - -
502C PRO* 4.8 2.2 - - - -
547C ARG 3.8 5.7 - - - +
548C VAL* 3.9 10.9 - - - +
549C HIS* 4.8 5.4 + - - -
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Residues in contact with LEU 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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410C LEU* 4.4 5.4 - - + -
443C VAL* 4.5 23.6 - - + +
454C LEU 4.0 1.6 + - - -
455C GLY* 1.3 73.3 - - - +
457C GLN* 1.3 64.1 + - - +
458C ILE* 4.6 0.4 - - + -
500C GLU* 3.1 2.8 - - - -
501C ILE* 2.8 58.0 + - + +
503C LEU* 3.5 31.0 - - + +
511C ALA* 4.2 16.2 - - + -
513C ILE* 4.7 2.7 - - + -
546C PHE* 3.5 31.9 - - + -
547C ARG 2.9 30.3 - - - +
548C VAL* 3.7 8.2 - - + +
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Residues in contact with GLN 457 (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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455C GLY 4.6 3.1 + - - +
456C LEU* 1.3 74.2 - - - +
458C ILE* 1.3 63.7 + - - +
459C PHE* 5.0 4.1 - - + -
492C ILE* 5.2 4.0 - - - +
498C VAL* 3.7 16.8 - - + +
499C LEU 2.8 10.5 - - - +
500C GLU* 3.5 28.9 + - + +
545C VAL 3.7 0.3 - - - +
546C PHE* 3.1 5.2 - - - -
547C ARG* 2.8 57.8 + - + +
549C HIS* 3.0 31.8 + - - -
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Residues in contact with ILE 458 (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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456C LEU* 4.6 1.3 - - + -
457C GLN* 1.3 76.9 - - - +
459C PHE* 1.3 66.2 + - - +
476C VAL* 4.2 8.2 - - + +
498C VAL* 3.2 1.6 - - - +
499C LEU* 2.7 70.7 + - + +
501C ILE* 4.3 24.2 - - + -
513C ILE* 4.3 11.7 - - + -
515C CYS* 5.2 0.4 - - - -
516C ALA* 4.2 20.0 - - + -
544C LEU* 5.4 5.4 - - + -
545C VAL 3.0 7.4 - - - +
546C PHE* 3.1 36.8 - - + -
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Residues in contact with PHE 459 (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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399C TRP 4.9 13.5 - - - -
457C GLN* 5.0 4.7 - - + -
458C ILE* 1.3 79.9 - - - +
460C ILE* 1.3 70.3 + - - +
461C GLY* 3.3 0.7 + - - -
468C LEU* 4.8 5.2 - - + -
470C PRO* 4.0 32.5 - - + -
476C VAL* 3.9 10.7 - - - +
496C THR* 5.8 3.6 - - - +
497C LYS 3.7 6.1 - - - +
498C VAL* 3.6 28.7 - - + -
544C LEU* 3.8 1.2 - - - +
545C VAL* 2.8 73.7 + - + +
547C ARG* 4.7 15.9 - - + -
561C GLN* 4.3 11.7 - - - -
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Residues in contact with ILE 460 (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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459C PHE* 1.3 73.3 - - - +
461C GLY* 1.3 58.6 + - - +
470C PRO* 3.9 3.8 - - - +
471C HIS* 3.0 23.1 + - + +
474C TYR* 3.8 25.4 - - + +
475C GLN* 4.1 3.3 - - - +
476C VAL* 3.6 32.1 - - + +
497C LYS 5.1 0.4 + - - -
518C ILE* 4.1 20.4 - - + -
542C VAL* 3.2 46.9 - - + -
543C ARG 4.2 0.7 - - - +
544C LEU* 3.4 33.7 - - + -
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Residues in contact with GLY 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C PHE* 3.3 4.8 + - - -
460C ILE* 1.3 76.3 - - - +
462C THR* 1.3 63.1 + - - -
468C LEU* 4.5 1.1 - - - -
469C LYS 3.5 10.1 - - - -
470C PRO* 4.1 3.8 - - - -
471C HIS* 3.6 4.2 - - - +
542C VAL* 3.6 12.3 - - - +
543C ARG 2.7 33.3 + - - +
545C VAL* 3.5 17.0 - - - +
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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