Contacts of the helix formed by residues 555 - 560 (chain B) in PDB entry 4DHZ
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 THR 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519B PRO 3.9 5.6 + - - -
520B SER* 3.2 25.5 - - - +
521B ASP 3.3 13.9 - - - +
522B THR* 3.8 10.8 - - + +
523B ILE* 4.6 6.3 - - - +
553B GLY 4.9 1.6 - - - +
554B ARG* 1.3 80.5 - - - +
556B LEU* 1.3 66.6 + - - +
557B SER* 3.4 15.6 + - - -
558B ASP* 3.0 29.0 + - - +
559B TYR* 3.5 9.5 + - - -
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Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B MET* 4.6 6.3 - - + -
503B ILE* 5.2 2.7 - - + -
517B VAL* 3.6 28.9 - - + -
518B GLU 3.5 22.7 - - - +
519B PRO* 3.9 11.6 + - + -
521B ASP* 3.2 14.4 + - + +
523B ILE* 4.5 9.4 - - + +
526B VAL* 4.3 18.2 - - + -
555B THR* 1.3 74.5 - - - +
557B SER* 1.3 61.1 + - - +
559B TYR* 3.2 4.3 + - - +
560B ASN 3.2 4.2 + - - -
561B ILE* 3.1 66.9 + - + +
567B LEU* 4.8 10.8 - - + -
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Residues in contact with SER 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B PRO* 3.3 29.8 + - - +
555B THR* 3.4 9.0 + - - -
556B LEU* 1.3 75.8 - - - +
558B ASP* 1.3 66.2 + - - +
560B ASN* 3.0 29.4 + - - +
561B ILE 4.9 2.2 - - - +
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Residues in contact with ASP 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ARG* 3.7 31.3 - - + +
555B THR* 3.0 31.0 + - - +
557B SER* 1.3 85.4 + - - +
559B TYR* 1.3 62.0 + - + +
560B ASN* 3.8 2.1 + - - -
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Residues in contact with TYR 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B ILE* 4.2 12.3 - - + -
545B PHE* 4.6 9.6 - - + -
548B LYS* 5.2 10.8 - - + -
549B GLN 3.7 8.8 + - - -
550B LEU* 3.7 29.6 - - + -
551B GLU* 3.0 45.5 + - - +
554B ARG* 4.0 23.6 - - + +
555B THR 3.5 15.6 + - - -
556B LEU 3.2 2.9 + - - +
557B SER 3.1 0.6 - - - -
558B ASP* 1.3 81.3 - - + +
560B ASN* 1.3 70.6 + - - +
561B ILE* 3.8 22.1 - - + +
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Residues in contact with ASN 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B PHE* 4.4 8.1 - - - -
556B LEU 3.2 0.2 + - - -
557B SER* 3.0 22.7 + - - +
558B ASP 5.3 1.5 + - - -
559B TYR* 1.3 82.8 - - - +
561B ILE* 1.3 62.5 + - - +
562B GLN* 3.8 21.6 + - - +
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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