Contacts of the strand formed by residues 874 - 882 (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 ARG 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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871A LEU* 5.4 0.2 - - - +
872A GLY* 2.9 17.5 + - - +
873A ASP* 1.3 100.9 + - - +
875A LEU* 1.3 61.5 + - - +
876A LEU 4.2 0.4 + - - -
898A GLU* 3.0 66.4 + - + +
899A LEU 3.2 13.5 + - - +
900A PRO* 3.9 20.0 - - + +
901A VAL* 4.3 1.1 - - - -
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Residues in contact with LEU 875 (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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774A LEU* 3.8 29.4 - - + -
782A LEU* 5.5 3.6 - - + -
805A PRO* 4.3 22.7 - - + -
808A LEU* 5.0 11.4 - - + -
865A VAL* 6.3 1.3 - - + -
871A LEU* 4.2 21.5 - - + -
874A ARG* 1.3 74.3 - - - +
876A LEU* 1.3 62.4 + - - +
877A LEU* 4.2 23.3 - - + -
897A LEU* 4.1 1.4 - - - +
898A GLU* 3.8 1.7 - - - -
899A LEU* 3.1 39.0 + - + +
901A VAL* 4.2 21.3 - - + +
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Residues in contact with LEU 876 (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* 4.1 6.3 - - - +
805A PRO* 3.6 20.3 - - + +
839A THR* 6.0 6.1 - - + -
874A ARG 4.3 0.2 + - - -
875A LEU* 1.3 74.6 - - - +
877A LEU* 1.3 73.8 + - - +
878A THR* 4.4 14.1 - - + -
896A GLN* 5.7 11.2 - - + +
897A LEU 3.3 14.6 - - - +
898A GLU* 3.8 30.0 - - + +
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Residues in contact with LEU 877 (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* 3.1 45.2 - - + -
768A PHE* 3.7 28.0 - - + -
782A LEU* 5.3 5.2 - - + -
802A PHE* 4.9 8.7 - - + -
803A SER 3.0 19.1 - - - +
804A HIS* 4.6 8.7 - - + -
808A LEU* 5.8 4.7 - - + -
875A LEU* 4.2 20.6 - - + -
876A LEU* 1.3 80.6 - - - +
878A THR* 1.3 64.8 + - - +
896A GLN* 3.2 19.8 - - - -
897A LEU* 3.2 12.8 + - + +
899A LEU* 5.8 0.2 - - + -
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Residues in contact with THR 878 (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* 4.1 1.7 - - - -
802A PHE* 3.2 30.1 - - - +
803A SER* 2.9 34.0 + - - +
876A LEU* 4.4 9.0 - - + -
877A LEU* 1.3 79.9 - - - +
879A ALA* 1.3 63.9 + - - +
880A ASN* 4.1 13.5 + - - -
894A THR* 4.9 6.5 - - - -
895A PHE 3.2 10.8 - - - -
896A GLN* 3.5 26.5 - - + +
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Residues in contact with ALA 879 (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* 3.3 44.9 - - + +
766A PHE* 3.5 21.3 - - + -
800A ILE* 3.9 5.2 - - + -
801A THR 3.2 7.2 - - - -
802A PHE* 4.0 7.2 - - + -
878A THR* 1.3 80.7 - - - +
880A ASN* 1.3 65.4 + - - +
881A VAL 3.5 0.2 + - - -
894A THR* 3.7 1.0 - - - -
895A PHE 3.0 16.3 + - - +
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Residues in contact with ASN 880 (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 4.1 0.5 - - - +
800A ILE* 3.0 16.8 - - - +
801A THR* 3.0 36.1 + - + +
878A THR* 4.1 10.4 + - - -
879A ALA* 1.3 70.5 - - - +
881A VAL* 1.3 58.8 + - - +
892A LYS* 5.4 7.6 - - - +
893A THR 4.8 0.4 - - - -
894A THR* 2.8 35.6 - - - +
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Residues in contact with VAL 881 (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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762A LEU* 4.0 15.0 - - + +
763A GLY 4.0 8.1 - - - +
764A ILE* 3.2 34.8 - - + -
788A VAL* 3.8 24.7 - - + -
798A THR* 4.6 7.2 - - - +
799A THR 3.8 9.9 - - - +
800A ILE* 4.0 10.3 - - + -
879A ALA 3.5 0.4 + - - -
880A ASN* 1.3 76.5 - - - +
882A SER* 1.3 68.4 + - - +
887A THR* 5.0 2.3 - - - +
893A THR* 3.3 32.0 + - + +
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Residues in contact with SER 882 (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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762A LEU* 3.6 11.2 - - - +
798A THR* 3.1 21.0 + - - -
799A THR* 3.2 24.9 + - - -
881A VAL* 1.3 76.7 - - - +
883A SER* 1.3 69.9 + - - +
886A ASN* 4.3 5.8 - - - -
887A THR* 3.3 34.0 - - - +
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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