Contacts of the strand formed by residues 410 - 419 (chain B) in PDB entry 1JN5
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 TYR 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B TYR* 2.7 41.9 + + - -
406B LEU* 3.2 29.2 + - + +
407B LEU 3.6 13.0 - - - +
408B ASP 3.4 1.8 - - - -
409B ALA* 1.3 81.9 - - + +
411B HIS* 1.3 66.0 + - - +
412B ASP* 3.8 0.9 + - - +
414B ALA* 3.9 8.7 - - + -
415B CYS 4.9 1.6 - - - -
459B ARG* 3.6 27.2 + - + -
462B VAL* 3.6 25.4 - - + -
463B VAL* 4.0 9.4 - - + -
466B LEU* 3.5 15.2 - - + +
517B PHE* 4.5 0.9 - - - -
528B CYS* 4.0 3.8 - - - -
529B ILE* 3.5 35.0 - - + -
532B ASP* 2.8 27.0 + - + -
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Residues in contact with HIS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A HIS* 3.4 23.8 + + - -
83A GLU* 2.7 41.1 + - - -
410B TYR* 1.3 76.7 - - - +
412B ASP* 1.3 76.1 + - + +
413B GLY* 2.9 31.3 + - - -
414B ALA* 3.0 17.2 + - + +
459B ARG* 3.5 6.9 - - - +
520B VAL* 4.8 0.2 - - - +
528B CYS* 3.4 25.7 - - - -
529B ILE 3.1 10.1 + - - +
530B VAL* 3.6 24.4 - - + +
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B TYR 4.8 0.7 - - - +
411B HIS* 1.3 81.8 + - + +
413B GLY* 1.3 58.1 + - - +
458B THR* 2.9 27.7 - - - +
459B ARG* 3.1 37.0 + - - +
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Residues in contact with GLY 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A HIS* 3.7 18.3 - - - -
411B HIS* 2.9 16.5 + - - -
412B ASP* 1.3 77.0 - - - +
414B ALA* 1.3 61.9 + - - +
415B CYS* 3.9 2.9 + - - -
457B HIS* 3.1 31.4 + - - -
458B THR* 4.0 3.6 - - - -
530B VAL 4.6 0.3 - - - +
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B TYR* 3.9 17.9 - - + -
411B HIS* 3.0 21.5 + - - +
412B ASP 3.4 1.2 + - - -
413B GLY* 1.3 78.2 - - - +
415B CYS* 1.3 59.5 + - - +
457B HIS* 3.5 1.4 - - - -
458B THR* 2.8 29.0 + - - +
462B VAL* 3.4 8.8 - - + +
529B ILE 3.3 25.6 - - - +
530B VAL* 3.4 13.5 - - - +
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Residues in contact with CYS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.7 33.7 - - - -
78A GLN* 3.8 19.5 - - - +
79A PRO* 4.4 9.4 - - - -
410B TYR* 4.9 1.2 - - - -
413B GLY 4.5 2.7 - - - -
414B ALA* 1.3 75.3 - - - +
416B CYS* 1.3 64.8 + - - +
455B LEU* 4.2 13.5 - - + -
456B LYS 3.3 5.8 - - - +
457B HIS* 3.7 10.1 - - - -
462B VAL* 4.1 1.8 - - - +
530B VAL 3.0 8.4 + - - -
531B ASN* 3.7 14.9 - - - +
532B ASP* 3.1 25.0 + - - +
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Residues in contact with CYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLN* 3.6 1.8 - - - +
415B CYS* 1.3 77.2 - - - +
417B SER* 1.3 68.1 + - - +
455B LEU* 3.5 1.1 - - - +
456B LYS* 2.8 41.2 + - + +
462B VAL* 3.8 26.0 - - + -
465B PHE* 4.2 23.6 - - - -
466B LEU* 4.3 12.1 - - - -
515B ARG* 4.9 0.7 - - - -
532B ASP* 3.2 32.5 - - + +
534B LEU* 5.7 2.7 - - - -
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 2.7 27.3 + - - -
78A GLN* 2.7 23.8 + - - +
416B CYS* 1.3 82.1 - - - +
418B LEU* 1.3 62.0 + - - +
440B ARG* 3.9 15.7 - - - -
454B LEU 4.5 7.0 - - - -
455B LEU* 3.7 11.9 - - - -
456B LYS* 5.4 0.7 - - - +
465B PHE* 5.2 3.1 - - - -
532B ASP 3.3 3.5 + - - +
533B GLU* 3.5 5.1 - - - +
534B LEU* 3.0 25.1 + - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 4.6 0.7 - - - -
417B SER* 1.3 76.0 - - - +
419B SER* 1.3 64.3 + - - +
420B ILE* 4.5 1.3 - - + -
435B TYR* 3.7 42.6 - - + +
438B ASP* 3.3 16.5 + - + +
439B SER* 3.3 4.9 - - - -
440B ARG* 2.7 32.8 + - - +
456B LYS* 5.9 0.6 - - - +
465B PHE* 4.2 28.3 - - + -
469B LEU* 4.7 4.7 - - + -
533B GLU* 3.9 1.3 - - - -
534B LEU* 3.1 35.2 - - + +
536B VAL* 3.7 31.6 - - + -
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 4.0 18.7 - - - +
76A ASP* 4.5 3.8 - - - +
94A VAL* 5.0 2.1 - - - +
418B LEU* 1.3 74.8 - - - +
420B ILE* 1.3 64.1 + - - +
439B SER* 3.9 4.7 - - - -
440B ARG 3.6 20.4 - - - +
441B ASN* 5.8 0.2 - - - -
533B GLU* 3.2 20.5 + - - -
534B LEU 2.9 6.3 + - - -
535B PHE* 3.1 22.4 - - - +
536B VAL 3.0 24.4 + - - -
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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