Contacts of the helix formed by residues 698 - 708 (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 698 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B TRP* 3.8 35.1 - - + +
444B MET 4.9 2.9 + - - +
445B PHE* 3.0 29.8 + - + +
696B PHE* 3.4 8.1 - - + -
697B MET* 1.3 71.4 - - - +
699B PRO* 1.4 67.3 - - - +
700B GLY* 2.9 27.9 + - - -
701B MET* 3.1 25.8 + - + +
702B GLU* 2.9 23.7 + - - +
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Residues in contact with PRO 699 (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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436B TRP* 4.0 32.3 - - + +
696B PHE* 4.0 10.8 - - + -
697B MET 3.1 6.2 - - - +
698B ASN* 1.4 89.2 - - - +
700B GLY* 1.3 55.6 - - - +
702B GLU* 3.5 17.1 - - + +
703B ARG* 3.1 52.2 + - - +
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Residues in contact with GLY 700 (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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698B ASN* 2.9 9.7 + - - -
699B PRO* 1.3 78.5 - - - +
701B MET* 1.3 58.9 + - - +
703B ARG* 3.3 21.3 + - - +
704B LEU* 3.0 26.0 + - - +
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Residues in contact with MET 701 (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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445B PHE* 6.0 5.6 - - + -
697B MET* 4.3 16.8 - - + -
698B ASN* 3.1 27.7 + - + +
700B GLY* 1.3 72.4 - - - +
702B GLU* 1.3 64.8 + - - +
704B LEU* 3.3 27.5 + - + +
705B ILE* 3.1 61.3 + - + +
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Residues in contact with GLU 702 (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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697B MET* 3.5 37.7 + - + +
698B ASN 2.9 19.1 + - - +
699B PRO* 3.5 17.2 - - + +
701B MET* 1.3 77.3 - - - +
703B ARG* 1.3 54.7 + - + +
705B ILE* 3.5 4.3 + - - +
706B SER* 2.6 35.1 + - - -
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Residues in contact with ARG 703 (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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699B PRO* 3.1 44.3 + - - +
700B GLY* 3.3 16.9 + - - +
702B GLU* 1.3 78.0 - - + +
704B LEU* 1.3 58.8 + - - +
706B SER* 3.8 4.7 + - - -
707B HIS* 2.9 34.6 + - + +
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Residues in contact with LEU 704 (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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700B GLY 3.0 14.4 + - - +
701B MET* 3.3 35.2 + - + +
703B ARG* 1.3 75.8 - - - +
705B ILE* 1.3 58.7 + - + +
707B HIS* 4.0 4.1 - - + +
708B HIS* 3.0 59.5 + - + +
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Residues in contact with ILE 705 (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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697B MET* 3.5 30.5 - - + -
701B MET* 3.1 37.6 + - + +
702B GLU* 4.1 4.9 - - - +
703B ARG 3.3 0.2 - - - -
704B LEU* 1.3 75.0 - - + +
706B SER* 1.3 62.5 + - - +
707B HIS 3.1 1.6 - - - -
708B HIS* 3.1 28.8 + - - +
709B HIS* 3.8 7.8 - - - +
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Residues in contact with SER 706 (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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702B GLU 2.6 25.5 + - - -
703B ARG* 3.8 4.7 + - - -
705B ILE* 1.3 77.9 - - - +
707B HIS* 1.3 60.6 + - - +
709B HIS* 4.1 21.4 + - - +
710B HIS* 4.6 4.7 + - - -
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Residues in contact with HIS 707 (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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703B ARG 2.9 22.4 + - - +
704B LEU* 4.0 5.5 - - - +
706B SER* 1.3 75.1 - - - +
708B HIS* 1.3 59.6 + - - +
709B HIS 2.8 12.5 + - - -
710B HIS* 3.0 41.9 + + + +
711B HIS* 3.9 26.7 + + - -
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Residues in contact with HIS 708 (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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704B LEU* 3.0 48.3 + - + +
705B ILE* 3.1 13.1 + - - +
707B HIS* 1.3 75.6 + - - +
709B HIS* 1.3 66.4 + - - +
711B HIS* 3.6 48.2 - + + +
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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
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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