Contacts of the helix formed by residues 520 - 529 (chain B) 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 ASP 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B PRO* 3.4 5.5 - - - +
519B SER* 1.3 84.1 + - - +
521B ILE* 1.3 77.5 + - - +
522B GLU* 3.1 32.3 + - - +
523B GLU* 3.2 18.3 + - + +
524B TYR 3.1 16.6 + - - -
551B ILE* 3.8 3.4 - - - -
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Residues in contact with ILE 521 (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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519B SER 4.2 0.4 + - - -
520B ASP* 1.3 79.0 + - - +
522B GLU* 1.3 68.3 + - + +
524B TYR* 3.2 26.6 + - + +
525B VAL* 2.8 29.9 + - + +
551B ILE* 3.8 16.5 - - + +
554B ASP* 3.6 39.1 + - + +
555B LEU* 3.8 29.8 - - + +
558B LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ASP* 3.1 21.7 + - - +
521B ILE* 1.3 87.6 - - + +
523B GLU* 1.3 56.4 + - - +
525B VAL* 3.5 8.5 + - - +
526B HIS* 3.1 26.9 + - - +
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Residues in contact with GLU 523 (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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498B ALA* 3.1 22.7 - - - +
518B PRO* 3.3 21.4 - - + +
519B SER 5.1 0.7 + - - -
520B ASP* 3.2 19.9 + - + +
522B GLU* 1.3 75.1 - - - +
524B TYR* 1.3 66.3 + - - +
526B HIS* 3.2 6.6 + - + +
527B ARG* 2.8 58.4 + - + +
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Residues in contact with TYR 524 (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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416B GLN* 2.5 41.8 + - - +
418B VAL* 4.4 5.2 - - - +
514B ASN* 3.5 12.3 - - - -
517B LEU* 3.7 22.9 - - + -
518B PRO* 3.5 15.9 - - + +
520B ASP 3.1 7.6 + - - +
521B ILE* 3.2 32.1 - - + +
523B GLU* 1.3 76.5 - - - +
525B VAL* 1.3 66.3 + - - +
527B ARG* 3.2 5.6 + - - +
528B ILE* 3.0 42.3 + - + +
540B ALA* 5.0 1.7 + - - +
542B SER* 3.4 25.7 + - - -
551B ILE* 4.3 2.9 - - + -
555B LEU* 3.8 22.2 - - + +
558B LEU* 4.0 11.9 - - + -
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Residues in contact with VAL 525 (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 THR* 3.7 33.8 - - + +
411B SER* 5.3 3.8 - - - +
521B ILE* 2.8 26.9 + - + +
522B GLU* 3.7 8.5 - - - +
524B TYR* 1.3 73.3 - - - +
526B HIS* 1.3 58.7 + - - +
528B ILE* 3.4 8.7 + - + +
529B GLY 2.9 24.6 + - - -
558B LEU* 3.4 31.2 - - + -
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Residues in contact with HIS 526 (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 THR* 5.4 1.3 - - - -
522B GLU 3.1 17.9 + - - +
523B GLU* 3.2 8.3 + - + +
525B VAL* 1.3 79.2 - - - +
527B ARG* 1.3 64.1 + - + +
529B GLY* 3.8 5.8 + - - -
530B ARG* 3.2 47.3 + - - +
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Residues in contact with ARG 527 (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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446B PHE* 3.6 52.2 - - + +
447B VAL 4.5 10.3 + - - -
448B GLU* 5.6 2.6 - - - +
498B ALA* 4.3 9.4 - - + +
512B VAL* 3.7 10.6 - - + +
514B ASN* 3.0 24.9 + - - +
516B ASP* 2.9 27.9 + - - +
517B LEU 4.5 0.6 - - - -
518B PRO* 3.4 25.9 - - - +
523B GLU* 2.8 50.6 + - + +
524B TYR* 3.2 7.6 + - - +
526B HIS* 1.3 77.7 - - + +
528B ILE* 1.3 64.4 + - + +
530B ARG* 3.1 23.5 + - - +
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Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B THR* 5.4 0.9 - - + -
411B SER* 4.0 18.2 - - - -
414B ILE* 3.4 12.4 - - + +
416B GLN* 3.6 37.0 - - + +
512B VAL* 4.5 7.2 - - + -
514B ASN* 3.8 11.9 - - - +
524B TYR* 3.0 46.0 + - + +
525B VAL* 3.5 13.5 - - + +
527B ARG* 1.3 72.0 - - - +
529B GLY* 1.3 61.6 + - - +
530B ARG 2.9 10.8 + - - -
531B THR* 3.1 24.1 - - - +
540B ALA* 3.6 26.0 - - + -
558B LEU* 5.1 0.9 - - + -
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Residues in contact with GLY 529 (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 THR* 3.5 27.1 - - - -
414B ILE* 4.2 7.6 - - - +
507B SER* 5.2 4.0 - - - -
525B VAL 2.9 11.6 + - - -
526B HIS* 4.2 4.0 - - - -
527B ARG 3.2 0.8 - - - -
528B ILE* 1.3 74.5 - - - +
530B ARG* 1.3 61.6 + - - +
531B THR 3.3 6.0 + - - +
532B GLY 5.2 2.1 - - - +
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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