Contacts of the helix formed by residues 509 - 517 (chain B) in PDB entry 1JEQ
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 GLN 509 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 5.3 10.8 - - - +
43B GLN* 5.8 1.5 + - - +
488B GLN* 4.1 3.1 - - - +
489B ARG* 5.4 0.2 - - - -
492B GLN* 3.0 46.6 + - - +
507B PRO 4.2 0.4 - - - -
508B ILE* 1.3 77.3 - - - +
510B GLN* 1.3 67.3 + - - +
511B HIS* 3.6 32.1 + - + +
512B ILE* 2.8 39.8 + - + +
513B TRP* 3.4 4.1 + - - -
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Residues in contact with GLN 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 5.6 4.1 - - - +
184B ARG* 5.5 2.8 - - - +
185B LEU* 6.5 0.2 - - + -
508B ILE 3.6 3.4 + - - -
509B GLN* 1.3 71.3 - - - +
511B HIS* 1.3 52.8 + - - +
513B TRP* 2.8 27.3 + - - +
514B ASN* 2.7 71.7 + - - +
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Residues in contact with HIS 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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36B LYS* 3.5 35.9 - - + +
40B MET* 6.3 0.4 - - + -
185B LEU* 3.1 41.7 - - + +
186B GLY* 4.2 2.0 - - - -
231B LEU* 3.7 40.1 + - + +
488B GLN* 4.3 11.8 + - + -
509B GLN* 3.6 31.2 + - + -
510B GLN* 1.3 77.7 - - - +
512B ILE* 1.3 80.3 + - + +
514B ASN* 3.8 1.3 - - - +
515B MET* 3.2 24.2 + - - +
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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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340A PHE* 4.3 4.3 - - + -
485B PRO* 3.9 26.9 - - + +
488B GLN* 3.5 39.3 - - + +
489B ARG* 4.1 12.6 - - + +
508B ILE* 4.2 17.3 - - + -
509B GLN* 2.8 30.0 + - + +
511B HIS* 1.3 97.2 - - + +
513B TRP* 1.3 63.8 + - - +
515B MET* 3.1 25.5 - - + +
516B LEU* 3.3 13.8 + - + +
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Residues in contact with TRP 513 (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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340A PHE* 3.8 33.2 - + + -
341A ASP* 3.4 16.6 - - - -
399A ARG* 3.5 31.9 - - - -
408A PRO* 5.9 0.4 - - + -
508B ILE* 3.6 54.2 - - + +
509B GLN 3.4 4.9 + - - -
510B GLN* 2.8 30.8 + - - +
512B ILE* 1.3 74.5 - - - +
514B ASN* 1.3 59.0 + - - +
516B LEU* 3.2 18.5 + - + +
517B ASN* 2.6 36.0 + - - +
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Residues in contact with ASN 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 3.9 34.5 + - + +
185B LEU* 3.3 40.4 + - - +
186B GLY 4.0 1.8 - - - -
187B GLY* 3.9 11.6 - - - +
510B GLN* 2.7 50.0 + - - +
511B HIS* 3.9 0.6 - - - +
512B ILE 3.2 0.2 - - - -
513B TRP* 1.3 73.5 - - - +
515B MET* 1.3 59.8 + - - +
517B ASN* 3.4 23.5 + - - +
518B PRO 5.3 0.2 - - - +
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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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186B GLY* 3.1 21.1 + - - +
188B HIS* 2.8 23.9 + - - +
231B LEU* 3.8 7.6 - - - +
232B ARG* 3.7 32.5 - - + -
477B PHE* 4.2 0.5 - - - -
482B ILE* 3.3 35.4 - - + +
483B PRO* 3.5 15.9 - - + +
485B PRO* 4.3 16.8 - - + -
488B GLN* 3.5 20.9 - - - +
511B HIS* 3.2 14.7 + - - +
512B ILE* 3.1 25.1 - - + +
514B ASN* 1.3 75.1 - - - +
516B LEU* 1.3 66.0 + - + +
517B ASN 3.2 0.8 + - - -
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Residues in contact with LEU 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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340A PHE* 4.3 14.1 - - + -
348A MET* 3.0 20.4 - - - +
399A ARG* 3.4 18.1 + - - +
408A PRO* 4.5 9.2 - - + -
410A PHE* 3.2 36.4 - - + -
439A PHE* 4.7 0.4 - - + -
477B PHE* 4.0 0.7 - - - -
482B ILE* 4.3 13.9 - - + -
485B PRO* 3.6 46.2 - - + -
512B ILE* 3.3 21.8 - - + +
513B TRP* 3.2 15.9 + - + +
515B MET* 1.3 80.1 - - + +
517B ASN* 1.3 58.8 + - - +
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Residues in contact with ASN 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A MET* 5.7 0.5 - - - +
348A MET* 3.7 0.4 - - - +
399A ARG* 2.8 28.9 + - - -
188B HIS* 3.4 13.0 - - - -
477B PHE* 3.0 12.6 - - - -
513B TRP* 2.6 34.8 + - - +
514B ASN* 3.4 15.0 + - - +
515B MET 3.2 0.4 - - - -
516B LEU* 1.3 80.2 - - - +
518B PRO* 1.3 79.2 - - + +
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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
------------------------------------------------------------
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