Contacts of the strand formed by residues 442 - 446 (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 VAL 442 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C ILE* 3.3 2.8 - - - +
413C GLU* 2.5 36.7 + - + -
414C VAL* 2.9 42.4 + - + -
440C HIS 3.3 9.0 - - - +
441C PRO* 1.3 81.9 - - - +
443C VAL* 1.3 61.4 + - - +
510C ARG* 3.8 42.6 - - + +
511C ALA 3.5 11.9 - - - +
512C THR* 4.3 15.5 - - + +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.3 28.7 - - + -
411C ARG 3.0 19.5 - - - +
412C ILE* 3.4 32.3 - - + -
413C GLU 4.1 0.4 - - - +
441C PRO* 6.2 0.4 - - + -
442C VAL* 1.3 79.5 - - - +
444C GLN* 1.3 61.9 + - - +
456C LEU* 4.5 18.1 - - + +
503C LEU* 4.6 0.5 - - - +
509C MET 4.2 0.3 - - - +
511C ALA* 3.0 34.2 + - - +
513C ILE* 5.0 3.9 - - + +
546C PHE* 3.9 27.8 - - + -
562C THR* 5.6 0.2 - - - +
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Residues in contact with GLN 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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410C LEU* 3.5 7.8 - - - +
411C ARG 3.0 31.0 + - - -
413C GLU* 3.8 15.3 - - + +
443C VAL* 1.3 73.2 - - - +
445C LEU* 1.3 57.9 + - - +
446C HIS* 3.3 39.9 + - + -
503C LEU* 5.4 0.7 - - - -
508C ASN* 3.3 30.2 + - - +
509C MET 3.0 15.7 - - - +
510C ARG* 3.1 45.8 + - + +
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Residues in contact with LEU 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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408C TYR* 4.1 10.5 - - + -
409C GLU 3.1 28.0 - - - +
410C LEU* 4.4 12.1 - - + +
444C GLN* 1.3 74.1 - - - +
446C HIS* 1.3 81.5 + - - +
447C GLY 4.0 0.7 + - - -
448C TYR* 4.4 19.8 + - + +
454C LEU* 4.6 12.6 - - + -
503C LEU* 4.7 6.7 - - + +
508C ASN* 4.1 7.3 + - - +
509C MET* 2.8 39.7 + - + +
548C VAL* 4.4 15.5 - - + -
550C ILE* 3.9 26.0 - - + -
560C LEU* 4.4 3.4 - - + -
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Residues in contact with HIS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TYR* 3.7 10.6 - - - +
409C GLU* 2.9 29.8 + - + +
411C ARG* 2.7 41.7 + - + +
413C GLU* 2.9 22.6 + - - -
444C GLN* 3.3 38.3 + - + +
445C LEU* 1.3 89.1 - - - +
447C GLY* 1.3 62.5 + - - +
508C ASN* 6.3 0.2 - - - +
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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