Contacts of the strand formed by residues 648 - 653 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647A SER* 4.0 21.1 - - - +
648A ARG* 4.7 21.4 - - - +
629D TYR* 3.3 10.4 - - - -
630D LEU 3.0 24.7 + - - +
645D ASP* 3.3 48.8 + - - +
646D GLY 3.0 17.2 + - - -
647D SER* 1.3 81.6 + - - +
649D TRP* 1.3 65.2 + - - +
650D HIS* 3.5 24.3 - - + +
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Residues in contact with TRP 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ASP* 5.1 0.4 - - - +
599A PRO* 3.6 48.7 - - + -
600A ALA* 3.6 30.4 - - + +
629A TYR* 5.7 1.8 - + - -
647A SER* 5.3 2.1 + - - -
600D ALA* 5.3 6.2 + - - +
604D LEU* 3.5 32.5 - - + -
606D ARG* 3.9 22.0 - - - -
607D GLN* 4.6 2.5 - - - -
627D GLN* 3.8 23.6 - - + -
628D PHE* 3.4 27.8 - - - -
629D TYR* 3.7 25.3 - + + +
648D ARG* 1.3 80.7 - - - +
650D HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627D GLN* 3.2 6.9 - - - +
628D PHE* 2.8 57.2 + + + -
630D LEU* 3.6 26.7 - - + +
644D LEU* 3.9 32.4 - - + +
645D ASP 3.0 30.4 + - - -
648D ARG* 3.5 32.1 + - + +
649D TRP* 1.3 75.7 + - - +
651D LYS* 1.3 62.0 + - - +
652D GLN* 5.1 2.0 - - + -
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Residues in contact with LYS 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625D ASP* 3.9 26.0 + - - +
626D VAL 3.5 4.9 - - - +
627D GLN* 3.7 34.3 - - + +
650D HIS* 1.3 73.3 - - - +
652D GLN* 1.3 73.7 + - - +
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Residues in contact with GLN 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625D ASP* 3.5 6.6 - - - +
626D VAL* 2.9 36.0 + - + +
628D PHE* 3.7 24.7 - - + -
642D ASP* 4.3 1.0 - - - +
644D LEU* 3.5 18.2 - - - +
650D HIS* 4.2 2.6 + - + -
651D LYS* 1.3 84.3 - - - +
653D GLN* 1.3 62.6 + - - +
654D HIS* 2.8 32.4 + - + +
660D PRO* 3.9 2.8 - - - +
662D TYR* 2.8 28.8 + - - -
2003D MPO 4.1 25.0 - - - +
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Residues in contact with GLN 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D ALA* 3.7 23.5 + - - +
624D GLY 3.2 6.5 - - - +
625D ASP* 2.9 27.1 - - - +
652D GLN* 1.3 77.6 - - - +
654D HIS* 1.3 72.2 + - - +
2003D MPO 3.6 21.0 + - - +
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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