Contacts of the helix formed by residues 508 - 522 (chain B) in PDB entry 4JWE
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 ASN 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A GLN* 5.1 9.1 + - - +
506B GLY 3.9 1.4 + - - -
507B LEU* 1.4 74.7 - - - +
509B GLU* 1.3 58.0 + - - +
510B ASP* 3.2 8.5 + - - +
511B GLU* 2.8 49.2 + - - +
512B ILE* 2.9 29.3 + - - +
14D ARG* 3.5 42.0 + - - +
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Residues in contact with GLU 509 (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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508B ASN* 1.3 73.2 - - - +
510B ASP* 1.3 63.6 + - - +
512B ILE* 3.3 21.6 + - + +
513B GLN* 3.3 24.5 + - - +
14D ARG* 3.5 19.8 + - - +
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Residues in contact with ASP 510 (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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508B ASN* 3.2 8.6 + - - +
509B GLU* 1.3 77.3 - - - +
511B GLU* 1.3 62.9 + - + +
512B ILE 3.5 0.2 + - - -
513B GLN* 3.5 22.4 + - - +
514B LYS* 3.3 25.3 + - - +
517B ARG* 5.3 2.6 + - - -
14D ARG* 3.9 38.3 - - + +
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Residues in contact with GLU 511 (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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402A GLU* 5.3 6.1 - - - +
439A HIS* 5.4 6.9 - - - -
449A ALA* 5.9 2.6 - - - +
506B GLY 4.5 1.6 - - - +
507B LEU* 3.5 33.6 - - + +
508B ASN* 2.8 50.3 + - - +
510B ASP* 1.3 75.7 - - + +
512B ILE* 1.3 59.3 + - - +
514B LYS* 3.6 14.3 - - + +
515B MET* 3.0 29.8 + - - +
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Residues in contact with ILE 512 (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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396B PRO* 3.6 38.4 - - + +
397B LEU* 3.7 35.8 - - + +
442B GLN* 5.4 0.2 - - - +
507B LEU* 3.3 24.0 - - + +
508B ASN 2.9 19.5 + - - +
509B GLU* 3.6 16.2 - - + +
510B ASP 3.3 0.4 - - - -
511B GLU* 1.3 76.6 - - - +
513B GLN* 1.3 58.0 + - - +
515B MET* 3.2 4.7 + - - +
516B VAL* 3.0 31.7 + - + +
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Residues in contact with GLN 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLU* 3.3 21.8 + - - +
510B ASP* 3.5 26.3 + - - +
512B ILE* 1.3 77.6 - - + +
514B LYS* 1.3 55.5 + - - +
516B VAL* 3.4 8.1 + - - +
517B ARG* 3.0 59.1 + - - +
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLY* 6.3 2.1 - - - -
510B ASP* 3.3 21.4 + - - +
511B GLU* 3.6 15.3 - - + +
513B GLN* 1.3 74.3 - - - +
515B MET* 1.4 56.5 + - - +
517B ARG* 3.4 19.9 + - - +
518B ASP* 2.9 33.2 + - + +
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Residues in contact with MET 515 (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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397B LEU* 3.8 21.5 - - + -
442B GLN 4.3 0.4 - - - +
443B GLY* 3.9 8.7 - - - -
444B GLU* 3.5 26.0 - - + +
445B ARG* 4.0 17.3 - - - -
450B ASP 3.5 23.8 - - - +
451B ASN* 3.8 13.5 - - - +
452B LYS 4.7 0.7 - - - +
507B LEU* 4.0 20.9 - - + -
511B GLU 3.0 18.8 + - - +
512B ILE 3.2 5.1 + - - +
514B LYS* 1.4 72.6 - - - +
516B VAL* 1.3 64.6 + - - +
518B ASP* 3.4 7.5 + - - +
519B ALA* 3.0 22.3 + - - +
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Residues in contact with VAL 516 (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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396B PRO 5.2 1.6 - - - +
397B LEU* 4.0 17.9 - - + -
414B LYS* 4.0 30.3 - - + +
444B GLU* 4.7 5.6 - - + -
512B ILE* 3.0 22.5 + - + +
513B GLN* 3.4 10.1 + - - +
515B MET* 1.3 77.6 - - - +
517B ARG* 1.3 63.0 + - + +
519B ALA* 3.4 6.4 + - - +
520B GLU* 3.1 28.2 + - + +
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Residues in contact with ARG 517 (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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510B ASP* 5.3 2.4 + - - -
513B GLN* 3.0 56.4 + - - +
514B LYS* 3.8 23.6 - - - +
516B VAL* 1.3 77.1 - - + +
518B ASP* 1.3 56.6 + - - +
520B GLU* 3.4 12.6 + - - +
521B ALA* 3.0 29.1 + - - +
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Residues in contact with ASP 518 (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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536A ARG* 4.9 4.0 + - - -
577A LYS* 4.0 5.9 - - - +
579A GLU* 4.5 3.2 - - - +
445B ARG* 2.8 35.5 + - - +
450B ASP* 5.1 2.6 - - - +
514B LYS* 2.9 20.6 + - + +
515B MET* 3.4 10.2 + - - +
517B ARG* 1.3 73.5 - - - +
519B ALA* 1.3 58.0 + - - +
521B ALA* 3.3 4.9 + - - +
522B ASN* 3.0 53.2 + - - +
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Residues in contact with ALA 519 (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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444B GLU* 3.5 41.5 - - + +
445B ARG* 3.6 15.0 - - - +
515B MET 3.0 14.2 + - - +
516B VAL 3.7 4.5 - - - +
518B ASP* 1.3 71.6 - - - +
520B GLU* 1.3 59.8 + - - +
522B ASN 3.3 1.7 + - - -
523B ALA* 2.9 30.7 + - - +
526B ASP* 5.0 2.1 - - - +
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Residues in contact with GLU 520 (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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516B VAL* 3.1 22.7 + - + +
517B ARG* 3.6 11.6 - - - +
518B ASP 3.4 0.2 - - - -
519B ALA* 1.3 77.5 - - - +
521B ALA* 1.4 61.0 + - - +
522B ASN 3.4 0.7 + - - -
523B ALA* 3.4 17.1 + - - +
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Residues in contact with ALA 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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577A LYS* 3.9 40.2 - - + +
578A GLY* 6.0 0.2 - - - -
517B ARG 3.0 17.2 + - - +
518B ASP* 3.3 6.5 + - - +
520B GLU* 1.4 74.8 - - - +
522B ASN* 1.3 63.4 + - - +
523B ALA 3.5 0.6 + - - -
524B GLU* 5.3 1.2 + - - +
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Residues in contact with ASN 522 (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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577A LYS 2.9 23.2 + - - -
578A GLY* 3.6 21.5 - - - -
579A GLU* 4.3 6.3 + - - -
445B ARG* 3.6 31.4 + - - +
518B ASP* 3.0 37.7 + - - +
519B ALA 3.4 3.1 - - - -
521B ALA* 1.3 80.2 - - - +
523B ALA* 1.4 56.0 + - - +
524B GLU 3.4 2.9 + - - -
525B ALA* 3.4 17.1 + - + +
526B ASP* 2.9 30.7 + - - +
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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