Contacts of the strand formed by residues 613 - 619 (chain A) in PDB entry 5ON2
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 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A PHE* 3.6 3.3 - - - -
575A TYR* 2.7 75.9 + - + +
576A TYR* 5.1 2.7 - - - -
577A VAL* 5.6 4.7 - - + -
611A GLU 4.5 6.7 - - - +
612A LEU* 1.3 73.4 - - - +
614A TYR* 1.3 67.7 + - - +
615A THR* 3.5 5.4 + - + -
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Residues in contact with TYR 614 (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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572A ASP* 2.7 38.8 + - + -
573A ALA 3.9 4.7 - - - -
574A PHE* 3.4 29.6 - + + -
601A ILE* 3.7 46.0 - - + +
604A ALA* 5.1 3.8 - - + -
612A LEU 3.9 4.2 + - - -
613A VAL* 1.3 74.6 - - - +
615A THR* 1.3 61.4 + - - +
616A GLY* 3.4 34.9 + - - -
617A MET* 3.7 5.2 + - - +
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Residues in contact with THR 615 (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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573A ALA* 2.8 34.7 + - - +
575A TYR* 3.5 34.8 - - + -
583A ARG* 6.0 0.4 - - - +
585A TRP* 3.7 13.3 - - + -
613A VAL* 3.7 6.5 - - + +
614A TYR* 1.3 73.5 - - - +
616A GLY* 1.3 63.2 + - - +
617A MET 4.0 5.4 - - - +
618A SER* 5.0 3.1 + - - -
624A LYS* 5.3 5.2 + - - +
69B G 4.2 2.7 + - - -
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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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572A ASP* 3.7 0.2 - - - -
573A ALA* 3.4 22.7 + - - +
614A TYR* 3.4 34.3 + - - -
615A THR* 1.3 80.0 - - - +
617A MET* 1.3 65.1 + - - -
68B C 5.2 0.7 - - - -
69B G 3.5 11.0 - - - -
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Residues in contact with MET 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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570A LEU* 4.2 14.1 - - + +
571A ALA* 3.6 25.8 - - - -
572A ASP* 3.4 25.6 - - - +
595A ARG* 6.1 1.3 - - - +
614A TYR* 3.7 4.1 + - - +
615A THR 4.0 2.3 - - - +
616A GLY* 1.3 72.7 - - - -
618A SER* 1.3 62.0 + - - +
657A GLU* 3.4 44.4 - - + +
658A TRP 5.7 3.1 - - - +
68B C 4.9 6.2 + - - +
69B G 3.1 36.6 + - - +
70B G 4.6 1.0 + - - -
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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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570A LEU* 3.4 6.0 - - - -
571A ALA 2.8 32.6 + - - +
573A ALA* 3.5 11.3 - - - +
615A THR 5.0 2.9 - - - -
616A GLY 4.8 0.2 - - - -
617A MET* 1.3 78.3 - - - +
619A LYS* 1.3 63.7 + - - +
624A LYS* 3.5 34.5 - - - +
626A ASN* 3.4 15.8 + - - -
69B G 4.0 2.5 - - - -
70B G 3.3 16.2 - - - -
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Residues in contact with LYS 619 (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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532A GLU* 2.7 27.1 + - - +
568A MET* 4.1 21.3 - - + -
569A VAL 3.8 6.7 - - - -
570A LEU* 3.8 6.0 - - - +
618A SER* 1.3 80.1 + - - +
620A MET* 1.3 68.3 + - - +
621A SER* 3.4 19.5 + - - +
624A LYS* 4.8 7.0 - - + +
626A ASN* 3.5 6.8 + - - +
901A LSS 3.7 14.1 - - - +
70B G 3.1 19.3 + - - +
71B G 2.7 31.8 + - - +
75B C 3.3 26.8 + - - +
76B A 3.9 2.8 + - - -
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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