Contacts of the strand formed by residues 799 - 805 (chain A) in PDB entry 3K72
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 799 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A GLY 3.2 16.8 + - - +
798A THR* 1.3 76.5 + - - +
800A ILE* 1.3 62.0 + - - +
801A THR* 4.2 14.0 - - - +
843A SER* 5.9 1.1 - - - -
844A CYS 4.0 1.3 - - - -
845A ARG* 3.4 31.4 - - + +
880A ASN 4.1 0.5 - - - +
881A VAL* 3.8 3.5 - - - +
882A SER* 3.2 37.4 + - - +
883A SER 5.0 4.2 + - - +
884A GLU* 5.4 1.3 - - - -
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Residues in contact with ILE 800 (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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764A ILE* 2.9 37.2 - - + -
788A VAL* 6.2 1.3 - - + -
798A THR* 5.9 0.2 - - - +
799A THR* 1.3 75.3 - - - +
801A THR* 1.3 62.0 + - - +
802A PHE* 4.3 18.0 - - + -
827A LEU* 6.5 0.2 - - + -
842A THR 4.2 1.0 - - - +
843A SER 3.8 0.3 - - - -
844A CYS* 2.9 48.1 + - + +
846A ILE* 5.1 9.9 - - + -
859A PHE* 3.9 30.3 - - + -
879A ALA* 3.9 9.2 - - + -
880A ASN 3.0 27.6 - - - +
881A VAL* 4.0 8.1 - - + -
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Residues in contact with THR 801 (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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799A THR* 4.4 15.0 - - - +
800A ILE* 1.3 76.6 - - - +
802A PHE* 1.3 63.9 + - - +
841A SER* 3.8 12.0 + - - +
843A SER* 3.3 35.0 - - - +
844A CYS 4.4 0.2 - - - +
879A ALA* 3.2 5.9 - - - -
880A ASN* 3.0 51.1 + - + +
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Residues in contact with PHE 802 (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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766A PHE* 4.3 17.3 - + + -
784A ALA* 5.8 6.1 - - + -
786A VAL* 4.7 19.7 - - + -
800A ILE* 4.3 25.6 - - + -
801A THR* 1.3 75.7 - - - +
803A SER* 1.3 64.3 + - - +
804A HIS* 4.6 3.1 - - + -
840A TRP 4.1 0.2 - - - +
841A SER* 3.1 28.5 + - - -
842A THR* 3.1 30.6 + - - +
844A CYS* 5.1 8.7 - - - -
859A PHE* 4.8 4.3 - + - -
861A ALA* 4.7 16.4 - - + -
863A PHE* 3.9 28.0 - + + -
877A LEU* 4.9 9.0 - - + -
878A THR* 3.2 21.8 - - - +
879A ALA* 4.0 16.6 - - + -
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Residues in contact with SER 803 (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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802A PHE* 1.3 75.4 - - - +
804A HIS* 1.3 61.3 + - - +
839A THR* 5.8 5.6 - - - -
840A TRP 4.0 6.1 - - - -
841A SER* 4.7 2.7 - - - +
876A LEU* 4.5 6.6 - - - +
877A LEU* 3.0 28.1 - - - +
878A THR* 2.9 40.4 + - - +
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Residues in contact with HIS 804 (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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802A PHE* 4.4 4.0 - - + -
803A SER* 1.3 76.1 - - - +
805A PRO* 1.3 86.8 + - + +
808A LEU* 3.0 38.7 + - + +
809A SER* 4.4 0.2 - - - -
839A THR* 3.5 7.2 - - - +
840A TRP* 2.9 75.5 + + - +
842A THR* 3.1 46.9 - - + +
863A PHE* 3.8 11.8 - + + -
876A LEU 4.5 0.9 - - - -
877A LEU* 4.7 6.5 - - + -
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Residues in contact with PRO 805 (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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804A HIS* 1.3 102.5 + - + +
806A ALA* 1.3 56.5 + - - +
807A GLY* 2.7 17.6 + - - +
808A LEU* 3.5 17.9 + - + +
838A GLY 4.1 5.8 - - - +
839A THR* 4.3 10.5 - - + -
870A VAL 5.0 1.3 - - - +
871A LEU* 4.4 23.3 - - + -
875A LEU* 4.3 23.8 - - + -
876A LEU* 3.6 19.5 - - + +
877A LEU* 5.3 0.4 - - + -
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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