Contacts of the strand formed by residues 440 - 446 (chain S) in PDB entry 6O81
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 LYS 440 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146S LEU 5.0 3.4 - - - +
147S ASN* 3.0 44.4 + - - +
148S GLY* 4.4 5.1 - - - +
407S ASN 4.7 0.2 - - - +
408S ILE* 4.7 3.2 - - - -
438S GLY 4.0 0.4 + - - -
439S GLU* 1.3 72.7 - - - +
441S ILE* 1.3 60.0 + - - +
456S TRP* 6.2 3.4 - - + -
457S GLY 3.4 9.6 - - - +
458S GLN* 4.8 2.5 - - + +
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Residues in contact with ILE 441 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146S LEU 5.7 0.2 - - - -
373S ILE* 5.4 8.3 - - + -
406S VAL* 5.3 6.1 - - + -
407S ASN 4.6 3.6 - - - -
408S ILE* 4.7 16.2 - - + +
439S GLU* 3.2 6.9 + - + +
440S LYS* 1.3 71.7 - - - +
442S ALA* 1.3 65.8 + - - +
456S TRP* 3.6 2.4 - - - -
457S GLY* 2.9 34.7 + - - +
459S ILE* 5.4 8.7 - - + +
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Residues in contact with ALA 442 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S ALA* 4.3 25.4 - - + +
146S LEU 4.7 2.5 - - - +
147S ASN* 5.1 0.2 - - + -
405S MET 5.5 0.2 - - - +
406S VAL* 3.4 21.3 - - - +
407S ASN* 3.7 27.5 + - + +
440S LYS 4.0 1.4 + - - -
441S ILE* 1.3 78.1 - - - +
443S LEU* 1.3 64.3 + - - +
444S SER* 6.4 0.2 - - - -
453S LEU* 6.0 2.0 - - + -
455S GLY 3.6 11.0 - - - +
456S TRP* 4.1 16.4 - - + +
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Residues in contact with LEU 443 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404S LEU* 5.0 11.2 - - + -
405S MET 4.0 4.7 + - - -
406S VAL* 4.6 2.5 - - + +
441S ILE 5.5 0.2 - - - +
442S ALA* 1.3 79.1 - - - +
444S SER* 1.3 59.5 + - - +
453S LEU* 4.1 1.6 - - - -
454S ILE* 2.9 24.7 + - + +
455S GLY* 2.9 27.6 + - - +
456S TRP* 5.5 1.6 - - - -
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Residues in contact with SER 444 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143S ALA* 5.7 6.5 - - - -
404S LEU* 3.5 13.3 - - - +
405S MET* 3.2 45.0 + - - -
442S ALA* 6.4 0.2 - - - -
443S LEU* 1.3 74.1 - - - +
445S ARG* 1.3 64.9 + - - +
451S TRP* 4.5 6.5 - - - -
452S ARG 3.3 23.1 - - - -
453S LEU* 3.9 5.6 - - - -
454S ILE* 3.9 2.7 - - - +
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Residues in contact with ARG 445 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395S VAL* 4.4 3.5 - - - +
396S GLN* 3.3 51.6 + - - +
397S LYS 3.3 16.6 + - - -
398S LEU* 4.4 5.9 - - - +
399S SER 5.1 0.6 - - - +
402S GLU* 5.8 4.8 - - - +
403S VAL 5.0 9.9 + - - +
404S LEU* 5.9 0.4 - - + -
444S SER* 1.3 77.0 - - - +
446S ARG* 1.3 74.1 + - - +
447S VAL* 3.2 4.9 + - - +
451S TRP* 3.9 8.7 - - - -
452S ARG* 2.8 28.4 + - - +
454S ILE* 4.6 17.0 - - + +
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Residues in contact with ARG 446 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ASN* 3.2 19.8 - - - +
265B ASP* 3.0 29.9 + - + +
266B TYR* 3.4 30.5 + - - -
275B GLY* 5.7 0.2 - - - -
445S ARG* 1.3 81.0 - - - +
447S VAL* 1.3 63.4 + - - +
448S GLU 4.4 0.4 - - - +
449S LYS* 3.7 30.3 + - - +
450S HIS 3.3 24.1 - - - +
451S TRP* 3.1 52.7 - - + +
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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