Contacts of the strand formed by residues 648 - 653 (chain C) in PDB entry 1XSK
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 ARG 648 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647B SER* 3.8 21.3 - - - +
648B ARG* 4.4 28.0 - - - +
629C TYR* 3.4 12.0 - - - -
630C LEU* 3.0 28.8 + - - +
645C ASP* 3.5 38.4 + - - +
646C GLY 3.1 18.9 + - - -
647C SER* 1.3 82.6 + - - +
649C TRP* 1.3 71.3 + - - +
650C HIS* 3.8 13.8 - - + -
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Residues in contact with TRP 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASP* 5.0 1.1 - - - +
599B PRO* 3.5 51.4 - - + -
600B ALA* 3.5 30.6 - - + +
629B TYR* 5.6 2.7 - + - -
647B SER 5.1 0.8 + - - -
600C ALA* 5.2 6.5 + - + +
604C LEU* 3.6 32.1 - - + -
606C ARG* 4.1 18.2 - - - -
607C GLN* 5.0 1.1 - - - -
627C GLN* 3.8 27.4 - - + +
628C PHE* 3.4 25.8 - - - -
629C TYR* 3.7 24.7 - + + +
648C ARG* 1.3 83.3 - - - +
650C HIS* 1.3 70.5 + - - +
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Residues in contact with HIS 650 (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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627C GLN* 3.1 9.0 - - - +
628C PHE* 2.8 58.3 + + + +
630C LEU* 3.8 15.8 - - + +
644C LEU* 3.6 44.7 - - + +
645C ASP 3.2 28.2 + - - -
648C ARG* 3.8 28.5 - - + +
649C TRP* 1.3 75.5 + - - +
651C LYS* 1.3 60.8 + - - +
652C GLN* 4.2 3.4 - - + -
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Residues in contact with LYS 651 (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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625C ASP* 4.0 27.2 + - - +
626C VAL 3.4 6.1 - - - +
627C GLN* 3.7 35.2 - - + +
650C HIS* 1.3 73.5 - - - +
652C GLN* 1.3 70.1 + - - +
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Residues in contact with GLN 652 (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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625C ASP* 3.4 4.8 - - - +
626C VAL* 2.8 39.0 + - + +
628C PHE* 3.8 14.5 - - + -
642C ASP* 4.2 3.1 - - - +
644C LEU* 3.6 16.0 - - + +
650C HIS* 4.2 2.7 - - + -
651C LYS* 1.3 81.4 - - - +
653C GLN* 1.3 61.1 + - - +
654C HIS* 2.6 43.8 + - + +
660C PRO* 3.7 12.3 - - - +
662C TYR* 2.8 27.4 + - - -
2002C MPO 4.4 20.4 - - - +
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Residues in contact with GLN 653 (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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623C ALA* 3.4 27.3 + - - +
624C GLY 3.3 4.3 - - - -
625C ASP* 2.9 25.8 - - - +
652C GLN* 1.3 77.1 - - - +
654C HIS* 1.3 65.3 + - - +
2002C MPO 3.4 24.3 + - - +
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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