Contacts of the strand formed by residues 614 - 617 (chain N) in PDB entry 2JA7
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 SER 614 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612N GLU 4.6 0.9 - - - -
613N VAL* 1.3 77.7 - - - +
615N MET* 1.3 63.8 + - - +
616N ILE* 3.9 6.3 - - - +
625N LYS 3.9 0.3 - - - +
626N ILE* 3.2 2.3 - - - +
627N PHE* 2.7 55.6 + - - +
632N ARG* 3.4 10.5 + - - +
692N TYR 5.5 1.1 - - - -
694N ASP* 3.0 35.0 + - - -
697N GLU* 3.2 10.1 - - - -
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Residues in contact with MET 615 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554N ILE* 6.1 0.7 - - - -
597N MET* 3.9 29.3 - - + +
600N LEU* 3.9 22.4 - - - +
601N ARG* 4.1 32.7 + - + +
604N ARG* 3.5 29.9 - - - +
609N ILE* 4.3 21.8 - - - -
613N VAL* 4.4 2.9 - - + -
614N SER* 1.3 78.2 - - - +
616N ILE* 1.3 62.3 - - - +
617N ARG 4.4 0.3 + - - -
625N LYS 3.2 4.9 - - - -
626N ILE* 3.6 28.9 - - + -
697N GLU* 2.9 26.1 + - - +
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Residues in contact with ILE 616 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597N MET* 4.8 0.2 - - - -
601N ARG* 5.8 0.7 - - - +
614N SER* 3.9 9.9 - - - +
615N MET* 1.3 90.2 - - - +
617N ARG* 1.3 69.2 + - - +
618N ASP* 3.7 8.9 + - + +
623N GLU 3.6 1.0 - - - +
624N LEU* 3.5 7.5 - - - +
625N LYS* 2.6 55.0 + - + +
626N ILE* 4.9 0.2 - - - +
627N PHE* 5.2 2.2 - - + -
696N GLU* 4.0 21.3 - - + +
697N GLU* 3.1 42.0 - - + +
699N GLU* 5.7 1.6 - - + -
700N SER* 3.6 21.5 - - - +
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Residues in contact with ARG 617 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578N THR* 5.0 8.0 + - + +
593N PRO* 2.9 40.1 - - + +
594N ALA* 2.9 29.4 - - - +
597N MET* 3.8 33.5 - - + +
601N ARG* 5.0 8.7 + - - +
616N ILE* 1.3 77.8 - - - +
618N ASP* 1.3 59.3 + - - +
619N ILE* 3.1 48.3 + - + +
623N GLU 3.6 7.4 - - - +
624N LEU* 4.1 9.2 - - + +
700N SER* 4.3 13.4 + - - -
59U VAL* 5.3 1.2 - - - +
61U ASP* 3.3 29.3 + - - +
64U SER* 4.3 3.4 + - - -
65U ASP* 5.6 1.4 - - - +
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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