Contacts of the strand formed by residues 425 - 432 (chain A) in PDB entry 1SIW
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 GLU 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A TYR* 5.4 1.6 + - - -
423A GLN* 3.5 9.2 - - - +
424A ASP* 1.3 88.5 - - + +
426A ILE* 1.3 67.6 + - - +
427A ALA* 4.9 5.4 + - - +
457A VAL* 3.0 46.7 + - + +
459A ARG* 3.8 26.8 + - - +
469A LEU* 4.0 14.4 - - + +
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Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A GLN* 4.4 20.2 - - + +
425A GLU* 1.3 84.5 - - - +
427A ALA* 1.3 59.3 + - - +
428A GLU* 4.1 3.6 + - - +
454A LYS* 3.7 35.9 - - + -
455A LEU 3.4 10.5 - - - +
456A PRO* 4.7 1.1 - - + -
487A LEU* 3.8 28.3 - - + -
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 4.5 3.8 - - + -
349A TYR* 3.6 31.0 - - + -
425A GLU* 4.0 4.0 - - - +
426A ILE* 1.3 74.4 - - - +
428A GLU* 1.3 63.3 + - - +
429A VAL* 3.8 1.5 + - - -
454A LYS* 3.7 1.4 - - - -
455A LEU* 2.8 34.0 + - - +
457A VAL* 3.5 26.2 - - + +
469A LEU* 4.1 7.4 - - + -
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Residues in contact with GLU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLY 5.1 3.8 - - - +
348A TYR* 3.5 9.5 - - + +
349A TYR* 2.9 27.6 + - - +
426A ILE 5.1 3.4 - - - +
427A ALA* 1.3 75.7 - - - +
429A VAL* 1.3 61.5 + - - +
452A LEU* 3.5 34.5 - - + +
453A HIS 3.1 11.2 - - - +
454A LYS* 4.0 32.4 + - + -
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.8 30.7 - - + -
349A TYR* 3.3 13.2 - - + +
350A ALA* 4.1 1.1 - - - -
351A ALA* 3.9 22.9 - - + +
427A ALA 4.4 2.2 - - - +
428A GLU* 1.3 77.5 - - - +
430A GLY* 1.3 69.4 + - - +
431A PHE* 3.3 31.1 - - + -
452A LEU* 3.3 3.9 - - - -
453A HIS 2.9 29.4 + - - -
455A LEU* 3.9 27.1 - - + -
476A LEU* 4.9 2.2 - - + -
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A TYR* 4.0 7.4 - - - -
349A TYR 2.8 16.3 + - - +
350A ALA* 4.7 2.4 - - - -
351A ALA* 5.0 1.9 + - - +
429A VAL* 1.3 76.9 - - - +
431A PHE* 1.3 66.3 + - - -
432A PRO* 4.4 0.3 - - - +
450A VAL* 3.9 15.9 - - - -
451A LEU 3.7 5.2 - - - -
452A LEU* 4.5 2.5 - - - -
632A MET* 3.0 25.0 - - - +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A VAL* 3.3 35.4 - - + -
430A GLY* 1.3 78.2 - - - -
432A PRO* 1.3 74.3 - - + +
433A TYR 3.7 0.2 + - - -
450A VAL* 3.4 2.6 - - - +
451A LEU* 2.8 47.0 + - + +
453A HIS* 3.7 15.9 - + + +
455A LEU* 3.9 12.3 - - + -
476A LEU* 3.4 35.2 - - + -
479A ALA* 3.8 16.6 - - + -
480A ASN* 3.5 35.0 - - + +
632A MET* 3.7 2.7 - - - +
1058A LEU* 4.2 11.0 - - + -
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Residues in contact with PRO 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A GLY 4.4 0.4 - - - +
431A PHE* 1.3 89.7 - - + +
433A TYR* 1.3 60.2 + - - +
434A PHE* 3.8 21.1 - - + -
449A ASN 3.4 7.2 - - - +
451A LEU* 5.5 0.9 - - - +
480A ASN* 5.3 0.6 - - - +
502A TYR* 4.3 3.3 + - - -
630A SER* 3.9 7.4 - - - +
631A PRO* 3.6 28.7 - - + -
632A MET* 3.3 15.2 - - + -
1055A GLY* 4.4 14.8 - - - +
1057A SER* 6.1 0.9 - - - +
1060A VAL* 3.9 24.7 - - + +
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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