Contacts of the helix formed by residues 541 - 546 (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 GLY 541 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TRP 3.4 0.6 + - - -
253A GLY 3.2 15.4 + - - -
254A SER* 3.7 7.4 - - - -
540A VAL* 1.3 78.1 - - - +
542A ALA* 1.3 59.3 + - - -
543A GLY 3.0 11.3 + - - -
544A LEU* 3.1 11.4 + - - -
545A ASN 3.1 8.3 + - - -
554A TYR* 3.4 10.3 + - - -
577A TYR 4.2 4.9 - - - -
578A VAL* 4.0 12.1 - - - -
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Residues in contact with ALA 542 (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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253A GLY 3.6 1.0 + - - -
541A GLY* 1.3 65.7 - - - -
543A GLY* 1.3 64.4 + - - +
544A LEU 3.0 3.2 + - - -
545A ASN* 3.7 11.2 - - - +
546A HIS* 3.3 52.4 + - + +
577A TYR 5.0 0.2 + - - -
578A VAL* 3.7 10.0 - - + +
1091A PRO* 6.3 0.2 - - + -
1092A HIS* 3.7 21.8 - - + +
1218A ARG* 3.5 14.2 + - - +
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Residues in contact with GLY 543 (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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253A GLY* 3.0 25.2 + - - -
302A ASP* 4.9 3.1 - - - +
542A ALA* 1.3 78.5 - - - +
544A LEU* 1.3 66.2 + - - +
547A TRP* 2.8 23.2 + - - -
1218A ARG* 4.4 8.8 + - - +
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Residues in contact with LEU 544 (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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252A TRP* 3.5 38.6 - - + +
253A GLY* 3.7 15.3 - - - -
302A ASP* 3.9 20.4 - - + +
540A VAL* 3.8 6.5 - - + -
541A GLY 3.1 4.8 + - - +
543A GLY* 1.3 87.0 - - - +
545A ASN* 1.3 61.3 + - - +
546A HIS 3.3 2.7 + - - -
547A TRP* 3.6 9.4 + - - -
550A LEU* 3.7 8.1 - - - +
553A ASN* 3.3 40.0 + - + +
554A TYR* 3.9 12.8 - - + -
557A LEU* 3.7 30.7 - - + -
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Residues in contact with ASN 545 (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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221A CYS* 3.0 31.7 + - - -
222A ASP* 3.6 12.3 + - - +
223A LEU 3.4 17.2 + - - -
224A PRO* 3.4 11.1 - - - +
541A GLY 3.1 9.0 + - - +
542A ALA* 3.6 6.5 + - - -
544A LEU* 1.3 78.0 - - - +
546A HIS* 1.3 59.2 + - + +
547A TRP 3.4 0.9 - - - -
550A LEU* 3.0 38.5 - - - +
554A TYR* 3.2 38.5 - - - +
576A HIS* 4.0 7.2 - - + -
578A VAL* 4.9 1.5 - - + +
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Residues in contact with HIS 546 (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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220A TYR 3.7 13.8 + - - -
221A CYS* 3.1 37.8 + - + -
222A ASP* 3.9 8.0 + - - -
542A ALA* 3.3 34.1 + - + +
544A LEU 3.3 0.6 - - - -
545A ASN* 1.3 78.7 - - + +
547A TRP* 1.3 61.3 + - - +
578A VAL* 5.5 1.6 - - + +
722A LYS* 6.1 2.0 - - - -
1090A THR* 4.9 5.5 + - - -
1092A HIS* 4.0 15.0 - + - -
1163A HIS* 6.3 2.5 - + - -
1216A SER* 4.0 2.9 - - - -
1217A ASN* 3.2 14.3 + - - +
1218A ARG* 3.0 57.9 + - + +
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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