Contacts of the strand formed by residues 414 - 420 (chain A) in PDB entry 2JGN
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 ILE 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A SER* 3.1 19.8 + - - +
412A GLU 4.2 2.7 - - - -
413A ASN* 1.3 83.4 - - - +
415A THR* 1.3 74.3 + - - +
416A GLN* 3.1 24.3 + - + +
528A ILE* 3.4 38.4 - - + +
529A GLY* 4.3 5.6 - - - -
531A THR* 3.8 37.7 - - + +
532A GLY* 5.5 0.4 - - - -
538A GLY 3.6 6.5 - - - +
540A ALA* 4.0 13.5 - - + -
564A GLN* 3.5 5.5 - - - +
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Residues in contact with THR 415 (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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412A GLU 5.4 0.7 + - - -
413A ASN 4.1 0.8 - - - -
414A ILE* 1.3 70.4 - - - +
416A GLN* 1.3 62.1 + - - +
417A LYS* 3.6 30.7 - - + +
537A LEU* 4.0 20.4 - - - +
538A GLY 2.8 18.2 + - - -
539A LEU* 3.5 13.1 - - + +
540A ALA 2.9 26.7 + - - +
564A GLN* 3.4 6.5 - - - +
566C VAL 5.4 0.5 + - - -
567C PRO* 4.9 0.2 - - - +
568C SER* 4.2 25.6 + - - +
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Residues in contact with GLN 416 (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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411A SER* 2.8 32.9 + - - -
414A ILE* 3.1 27.8 + - + +
415A THR* 1.3 74.4 - - - +
417A LYS* 1.3 69.6 + - - +
418A VAL* 4.0 1.6 + - + -
524A TYR* 2.7 31.7 + - - +
528A ILE* 3.7 9.0 - - + +
540A ALA* 3.2 8.5 - - + +
558A LEU* 3.3 21.3 - - - +
559A LEU* 3.7 15.7 - - + +
564A GLN* 2.9 36.1 + - - +
565A GLU* 4.5 10.0 + - - +
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Residues in contact with LYS 417 (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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415A THR* 3.6 23.4 - - + +
416A GLN* 1.3 80.4 - - - +
418A VAL* 1.3 61.8 + - - +
419A VAL* 3.9 2.7 - - + -
539A LEU* 4.5 18.6 - - + +
540A ALA 2.9 6.1 + - - +
541A THR* 3.3 14.8 - - + +
542A SER 2.9 24.4 + - - -
565A GLU* 4.0 24.7 - - + +
533B ARG* 5.2 6.7 - - - +
535B GLY 3.4 23.3 + - - +
536B ASN* 4.2 22.8 - - - +
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Residues in contact with VAL 418 (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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416A GLN 4.0 0.8 + - - +
417A LYS* 1.3 75.6 - - - +
419A VAL* 1.3 65.1 + - - +
524A TYR* 4.7 4.7 - - - +
542A SER* 3.5 15.5 - - - +
544A PHE* 4.2 9.4 - - + -
555A LEU* 4.0 33.0 - - + -
559A LEU* 3.7 34.8 - - + -
565A GLU 5.6 2.0 + - - -
567A PRO* 3.5 24.9 - - + +
569A TRP* 3.8 26.4 + - + -
570A LEU* 4.8 4.3 - - + -
413B ASN* 4.7 0.3 - - - +
537B LEU* 5.8 1.9 - - - +
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Residues in contact with VAL 419 (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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417A LYS* 4.7 1.1 - - + -
418A VAL* 1.3 82.8 - - - +
420A TRP* 1.3 62.0 + - - +
421A VAL* 3.5 1.0 + - + -
429A PHE* 3.8 26.5 - - + -
541A THR* 4.0 11.4 - - + -
542A SER 2.9 14.7 + - - +
543A PHE* 3.5 11.0 - - + -
544A PHE* 2.9 25.3 + - - +
569A TRP* 4.0 4.5 - - - -
413B ASN* 3.4 22.7 - - + +
535B GLY* 4.0 27.8 - - - +
536B ASN* 4.1 11.4 - - - +
537B LEU* 5.6 1.8 - - + -
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Residues in contact with TRP 420 (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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419A VAL* 1.3 70.6 - - - +
421A VAL* 1.3 68.3 + - - +
422A GLU* 2.7 32.1 + - + -
429A PHE* 4.5 1.7 - - - -
544A PHE* 3.3 26.9 - + - -
545A ASN* 3.8 12.3 - - + +
546A GLU* 3.6 43.5 - - + -
569A TRP* 3.7 36.5 - + + +
573A MET* 3.7 27.4 - - + -
412B GLU* 3.6 39.6 + - + +
413B ASN* 2.7 34.1 + - - +
563B LYS* 5.1 4.7 - - + -
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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