Contacts of the strand formed by residues 614 - 618 (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 GLU 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A THR* 4.1 8.2 - - + +
588A GLU* 2.6 47.0 + - - +
591A HIS* 4.5 1.3 - - + +
592A LEU* 3.1 33.8 - - + +
596A ARG* 5.0 1.0 - - - +
607A ILE* 3.3 18.6 - - + +
608A LEU 3.3 13.5 - - - +
609A TYR* 3.5 13.9 - - + -
613A PHE* 1.3 77.4 - - - +
615A SER* 1.3 66.0 + - - +
626A TRP* 3.7 14.5 - - + -
627A THR* 3.4 2.9 - - - +
628A SER 2.7 34.1 + - - +
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ASP 3.4 0.2 - - - +
607A ILE* 3.4 5.2 - - - +
608A LEU* 2.9 52.9 + - - +
610A HIS* 4.1 5.7 - - - -
613A PHE* 4.5 5.8 - - - -
614A GLU* 1.3 79.1 - - - +
616A GLY* 1.3 58.2 + - - +
617A TYR 4.4 1.0 + - - -
624A PRO* 4.2 12.8 - - - +
626A TRP* 3.2 25.8 - - - -
627A THR* 4.0 13.7 - - - -
695A THR 4.9 1.8 + - - -
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Residues in contact with GLY 616 (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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605A TYR* 3.9 16.6 - - - -
606A ASP 3.4 6.5 - - - -
607A ILE* 4.5 0.2 - - - -
615A SER* 1.3 70.7 - - - +
617A TYR* 1.3 60.8 + - - -
618A SER 3.6 0.5 + - - -
624A PRO* 3.3 2.5 - - - +
625A LEU* 2.8 32.9 + - - +
626A TRP* 3.1 32.1 + - - -
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Residues in contact with TYR 617 (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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605A TYR* 3.1 3.7 - - - -
606A ASP* 2.7 48.8 + - + +
608A LEU* 3.6 21.5 - - + -
615A SER* 3.7 3.4 - - - +
616A GLY* 1.3 71.7 - - - +
618A SER* 1.3 72.1 + - - +
619A GLU* 3.6 3.1 + - - -
622A LEU* 3.3 21.6 + - - -
623A MET* 3.5 26.0 - - - -
624A PRO* 3.8 4.7 - - + -
654A VAL* 3.7 20.0 - - + -
658A PHE 2.6 29.7 + - - -
659A SER* 3.7 9.4 - - - -
660A GLN 4.3 1.0 + - - -
694A VAL 4.9 1.5 + - - -
695A THR* 3.4 46.8 - - + +
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Residues in contact with SER 618 (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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603A THR* 4.4 2.6 + - - -
604A SER 3.8 7.9 + - - -
605A TYR* 3.9 3.1 - - - -
616A GLY 3.6 1.8 + - - -
617A TYR* 1.3 83.9 - - - +
619A GLU* 1.3 56.1 + - - +
620A ILE* 3.1 8.4 + - - +
621A PHE* 2.9 32.1 + - - -
622A LEU* 3.0 19.1 + - - -
623A MET 2.9 19.5 + - - -
625A LEU* 3.5 26.5 - - - -
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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