Contacts of the strand formed by residues 839 - 845 (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 839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A SER* 5.8 4.5 - - - -
804A HIS 3.5 17.0 - - - +
805A PRO* 4.3 11.0 - - + -
833A PRO* 4.9 0.3 - - - +
834A VAL 3.7 1.0 + - - -
835A GLY* 3.3 32.7 + - - +
837A GLN 3.8 1.5 + - - -
838A GLY* 1.3 82.4 + - - +
840A TRP* 1.3 66.0 + - - +
876A LEU* 6.0 6.1 - - + -
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Residues in contact with TRP 840 (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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803A SER* 4.8 2.4 - - - -
804A HIS* 2.9 54.4 + + - +
806A ALA* 3.2 39.6 - - + +
808A LEU 3.7 0.4 - - - -
809A SER* 3.5 25.8 - - - -
831A SER* 5.0 8.3 - - - -
832A ALA* 3.2 21.1 - - - +
833A PRO* 3.3 43.5 - - + -
834A VAL* 3.6 10.1 - - - +
838A GLY 4.3 1.1 - - - -
839A THR* 1.3 82.3 - - - +
841A SER* 1.3 59.8 + - - +
842A THR* 6.0 0.2 - - + -
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Residues in contact with SER 841 (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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801A THR* 3.8 19.6 + - - +
802A PHE 3.1 15.4 + - - -
803A SER* 4.7 2.7 - - - +
830A ASP 4.0 1.9 - - - +
831A SER 3.7 0.5 - - - -
832A ALA* 3.0 34.9 + - - +
834A VAL* 3.4 19.5 - - - +
840A TRP* 1.3 73.2 - - - +
842A THR* 1.3 64.0 + - - +
843A SER* 3.9 4.7 + - - -
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Residues in contact with THR 842 (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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801A THR* 3.7 1.2 - - - -
802A PHE* 3.1 27.5 + - - +
804A HIS* 3.1 38.5 + - + +
809A SER* 4.8 0.7 - - - -
810A TYR* 4.5 22.0 - - + +
829A CYS* 5.9 0.7 - - - -
830A ASP 3.8 4.3 - - - -
831A SER* 3.2 34.1 - - - +
832A ALA 4.7 0.2 - - - +
840A TRP* 5.9 0.2 - - + -
841A SER* 1.3 75.6 + - - +
843A SER* 1.3 64.2 + - - +
844A CYS* 4.1 3.9 - - - -
863A PHE* 3.4 16.2 - - - -
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Residues in contact with SER 843 (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* 5.9 2.2 - - - -
801A THR* 3.3 29.8 - - - -
828A THR 4.6 0.2 - - - -
829A CYS* 3.4 0.2 - - - +
830A ASP* 3.0 45.9 + - - +
841A SER* 3.9 5.2 + - - -
842A THR* 1.3 74.4 - - - +
844A CYS* 1.3 66.0 + - - +
845A ARG 4.3 0.9 - - - -
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Residues in contact with CYS 844 (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* 4.5 0.6 - - - -
800A ILE* 2.9 49.1 + - + +
802A PHE* 5.1 10.3 - - + -
810A TYR* 4.6 10.1 - - - -
827A LEU* 4.6 6.6 - - + +
828A THR 3.3 7.6 - - - -
829A CYS* 2.0 52.5 - - - -
842A THR* 4.1 8.7 - - - -
843A SER* 1.3 79.3 - - - +
845A ARG* 1.3 62.8 + - - +
846A ILE* 3.5 1.6 + - - +
859A PHE* 5.9 2.5 - - + -
863A PHE* 6.3 0.7 - - - -
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Residues in contact with ARG 845 (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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710A PRO* 5.3 10.5 - - - +
797A GLY* 4.1 23.8 + - - +
798A THR 3.7 6.3 - - - +
799A THR* 3.4 27.0 - - + +
827A LEU* 4.7 0.4 - - - -
828A THR* 3.0 36.8 + - + +
843A SER* 4.3 0.6 - - - -
844A CYS* 1.3 71.4 - - - +
846A ILE* 1.3 53.5 + - - +
847A ASN* 2.7 62.4 + - - -
884A GLU* 4.9 4.9 + - - +
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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