Contacts of the strand formed by residues 726 - 733 (chain A) in PDB entry 3NKO
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 VAL 726 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A TYR 4.0 0.2 - - - +
630A THR* 3.5 5.6 - - - -
631A ILE* 2.8 42.6 + - + +
716A VAL* 3.9 11.9 - - + +
719A TYR* 3.8 24.9 - - + +
720A ALA* 3.9 17.5 - - + +
723A ARG* 4.0 15.0 - - - +
725A GLY* 1.3 80.6 - - - +
727A ASN* 1.3 59.5 + - - +
728A VAL* 4.0 13.7 + - + +
767A ILE* 3.5 31.4 - - + -
768A THR 3.5 4.9 - - - +
777A ALA* 4.1 2.0 - - - +
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Residues in contact with ASN 727 (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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591A HIS 3.2 24.0 + - - -
592A LEU* 5.8 0.2 - - - -
593A LEU* 3.8 13.7 - - + +
594A TYR* 3.3 43.0 - - + +
628A SER* 3.9 1.9 + - - -
629A TYR 3.5 8.5 + - - -
630A THR* 2.9 25.0 + - - +
726A VAL* 1.3 73.0 - - - +
728A VAL* 1.3 60.1 + - - +
729A ILE* 4.0 17.2 - - - +
766A ILE 3.5 2.3 - - - +
767A ILE* 3.4 4.2 - - - -
768A THR* 2.8 34.3 + - - +
777A ALA* 4.4 1.8 - - - +
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Residues in contact with VAL 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A THR 3.5 0.5 - - - +
628A SER* 3.2 4.2 + - - -
629A TYR* 2.8 76.5 + - + +
711A PHE* 5.1 2.2 - - + -
716A VAL* 4.1 11.4 - - + -
726A VAL* 4.0 21.5 - - + +
727A ASN* 1.3 77.9 - - - +
729A ILE* 1.3 67.4 + - - +
730A SER* 3.4 23.3 - - - +
765A SER* 3.4 12.1 - - - +
766A ILE 3.5 3.6 - - - +
767A ILE* 4.3 11.9 - - + -
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Residues in contact with ILE 729 (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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592A LEU* 5.1 4.9 - - + -
594A TYR* 5.5 7.0 - - + -
595A GLY 5.7 1.8 - - - +
597A PRO* 4.8 6.7 - - + -
626A TRP* 3.8 27.1 - - + -
627A THR 3.2 10.8 - - - +
628A SER* 3.7 20.2 - - - +
727A ASN* 4.0 12.1 - - - +
728A VAL* 1.3 78.8 - - - +
730A SER* 1.3 63.4 + - - +
764A TYR* 3.6 11.6 - - + +
765A SER* 3.3 1.2 - - - -
766A ILE* 2.8 48.4 + - + +
833A PHE* 3.9 31.0 - - + -
834A TYR* 6.4 1.6 - - + -
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Residues in contact with SER 730 (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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626A TRP* 3.4 3.3 - - - -
627A THR* 2.8 37.4 + - - -
629A TYR* 4.7 2.8 + - - -
676A LEU* 4.4 16.1 + - - -
708A TRP* 4.0 22.3 - - - -
711A PHE* 4.4 2.1 - - - -
712A GLN* 5.2 0.2 + - - -
728A VAL* 3.4 11.7 - - - +
729A ILE* 1.3 71.5 - - - +
731A GLY* 1.3 59.7 + - - +
764A TYR* 3.2 15.5 - - - -
765A SER* 2.9 23.4 + - - -
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Residues in contact with GLY 731 (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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625A LEU 4.1 0.9 - - - -
626A TRP* 4.6 0.4 - - - -
676A LEU* 4.2 9.0 - - - +
730A SER* 1.3 79.2 - - - +
732A PRO* 1.3 68.4 - - - +
763A TYR* 3.3 12.6 - - - -
764A TYR* 2.8 49.6 + - - +
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Residues in contact with PRO 732 (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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623A MET* 3.9 17.9 - - + -
624A PRO 3.0 28.5 - - - +
625A LEU* 4.0 11.8 - - + +
676A LEU* 4.5 6.5 - - + -
698A VAL* 5.4 0.2 - - + -
731A GLY* 1.3 87.6 - - - +
733A ILE* 1.3 66.1 - - - +
734A PHE* 4.0 13.2 - - + -
760A PRO* 3.5 26.9 - - + -
762A HIS 3.7 5.2 - - - +
763A TYR* 3.8 8.9 - - + -
764A TYR* 3.8 6.2 - - - -
829A THR* 4.0 5.7 - - - +
1013A EDO 6.1 0.5 - - - -
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Residues in contact with ILE 733 (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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732A PRO* 1.3 79.2 - - - +
734A PHE* 1.3 70.6 + - - +
735A ASP* 4.3 0.4 - - + +
760A PRO* 3.4 2.6 - - - +
761A THR* 2.8 28.2 + - - +
762A HIS* 2.8 30.9 + - + +
764A TYR* 3.8 30.1 - - + +
790A ILE* 4.0 22.0 - - + -
825A ILE* 4.6 3.6 - - + -
828A LEU* 3.8 46.2 - - + +
829A THR* 3.6 18.4 - - + -
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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