Contacts of the helix formed by residues 638 - 644 (chain B) in PDB entry 2JED
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 638 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636B GLU 3.7 4.0 + - - -
637B ILE* 1.3 70.6 - - - +
639B TRP* 1.3 59.1 + - - +
640B GLU* 3.1 26.4 + - - +
641B GLU* 3.0 51.7 + - - +
642B LEU* 3.1 23.0 + - - +
647B ILE* 3.5 13.2 - - + +
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Residues in contact with TRP 639 (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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486B ALA* 3.3 44.2 - - + -
489B ILE* 4.0 25.6 - - + -
490B LEU* 3.7 25.3 - - + +
629B ARG* 3.2 69.6 + - + +
630B GLN* 4.9 5.6 - - - -
634B PHE* 3.7 23.2 + + + +
637B ILE* 3.6 24.4 + - + +
638B ASN* 1.3 70.6 + - - +
640B GLU* 1.3 65.4 + - + +
642B LEU* 3.8 8.8 - - + +
643B GLU* 3.2 23.9 + - - +
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Residues in contact with GLU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B ASN* 3.4 20.3 + - - +
639B TRP* 1.3 79.9 - - + +
641B GLU* 1.3 63.4 + - + +
643B GLU* 3.5 5.1 + - - +
644B ARG* 3.4 51.5 + - - +
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Residues in contact with GLU 641 (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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638B ASN* 3.0 42.6 + - - +
640B GLU* 1.3 73.4 - - + +
642B LEU* 1.3 62.3 + - - +
644B ARG* 3.3 6.4 + - - +
645B LYS 3.2 3.6 + - - -
646B GLU* 2.9 57.9 + - + +
647B ILE* 4.0 18.6 - - + +
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Residues in contact with LEU 642 (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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440B PHE* 3.2 15.8 - - - -
483B PHE* 3.8 24.2 - - + -
486B ALA* 3.5 37.0 - - + +
487B GLU* 3.8 25.0 - - + +
490B LEU* 3.6 21.5 - - + -
637B ILE* 4.0 14.1 - - + -
638B ASN 3.1 16.9 + - - +
639B TRP* 3.8 8.1 - - + +
640B GLU 3.3 0.2 - - - -
641B GLU* 1.3 76.9 - - - +
643B GLU* 1.3 57.6 + - - +
645B LYS* 3.0 18.9 + - - -
647B ILE* 3.8 21.3 - - + +
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Residues in contact with GLU 643 (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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438B HIS* 2.9 35.3 + - + -
439B PRO* 3.4 26.2 - - + +
440B PHE* 4.1 2.2 - - - -
490B LEU* 3.6 30.7 - - + +
629B ARG* 4.7 5.3 + - - -
639B TRP 3.2 14.7 + - - +
640B GLU* 4.0 4.9 - - - +
641B GLU 3.4 0.2 - - - -
642B LEU* 1.3 76.9 - - - +
644B ARG* 1.3 62.1 + - + +
645B LYS 3.3 1.0 + - - -
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Residues in contact with ARG 644 (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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640B GLU* 3.4 45.7 + - - +
641B GLU* 3.3 10.4 + - - +
642B LEU 3.1 0.6 - - - -
643B GLU* 1.3 79.2 - - + +
645B LYS* 1.3 71.1 + - - +
646B GLU* 3.0 53.5 + - - +
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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