Contacts of the helix formed by residues 653 - 658 (chain B) in PDB entry 1ED8
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 653 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B ALA* 3.7 16.1 - - + +
650B GLU* 2.8 21.8 + - + +
652B GLN* 1.3 79.6 - - - +
654B ALA* 1.3 70.8 + - - +
655B THR 3.4 0.4 - - - -
656B PRO* 3.0 8.7 - - + +
657B ALA* 2.9 20.8 + - - +
666B ARG* 3.5 17.3 + - - -
669B TYR* 3.8 19.1 + - - +
763B ASN* 5.5 0.2 - - - -
828B LYS* 3.0 28.9 + - - -
952B ZN 3.7 0.5 - - - -
956B PO4 4.6 1.6 + - - -
962B MG 3.7 16.5 - - - -
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Residues in contact with ALA 654 (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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602B SER* 4.1 5.4 - - - -
603B ALA* 3.6 39.3 - - + +
606B ALA* 4.3 1.4 - - - +
620B LEU* 3.6 10.3 - - + +
652B GLN 3.6 1.2 + - - -
653B ASP* 1.3 78.9 + - - +
655B THR* 1.3 56.8 + - - +
657B ALA* 4.2 1.8 - - - -
658B ALA* 2.9 34.7 + - - +
666B ARG* 3.8 25.3 - - + +
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Residues in contact with THR 655 (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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549B ILE* 4.3 6.5 - - + -
551B ASP* 3.0 1.8 + - - +
602B SER* 2.6 18.4 + - - -
606B ALA* 4.2 5.6 - - - +
609B TRP* 4.0 23.7 - - + -
653B ASP 3.4 0.2 - - - -
654B ALA* 1.3 75.9 - - - +
656B PRO* 1.3 61.1 - - - +
658B ALA* 3.8 9.5 + - - +
659B LEU* 4.6 2.1 - - - +
820B GLN* 3.2 27.2 + - - +
822B GLU* 3.2 29.2 - - + +
869B ASP* 5.8 0.2 - - - +
952B ZN 2.2 4.3 - - - -
962B MG 2.2 29.4 - - - -
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Residues in contact with PRO 656 (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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645B ASN* 3.0 46.2 + - - +
647B SER* 3.8 26.0 - - - +
650B GLU 4.1 8.5 - - - +
651B LEU* 3.9 22.4 - - + +
653B ASP* 3.0 24.5 - - + +
655B THR* 1.3 89.4 - - - +
657B ALA* 1.3 63.3 + - - +
658B ALA 3.3 0.5 + - - -
659B LEU* 3.3 9.7 + - - +
660B VAL* 4.0 2.6 - - - +
695B LEU* 6.5 0.2 - - - -
820B GLN* 4.1 3.6 - - - +
822B GLU* 3.6 7.6 - - + +
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Residues in contact with ALA 657 (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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620B LEU* 3.9 15.0 - - + -
651B LEU 3.9 5.1 + - - +
652B GLN 3.5 15.5 - - - +
653B ASP 2.9 23.2 + - - +
654B ALA 3.3 2.6 + - - +
656B PRO* 1.3 78.6 - - - +
658B ALA* 1.3 56.3 + - - +
660B VAL* 3.1 10.1 + - - +
661B ALA* 2.9 31.7 + - - +
691B ILE* 3.8 17.9 - - + -
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Residues in contact with ALA 658 (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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606B ALA* 3.5 35.2 - - + +
607B THR* 4.2 4.7 - - - +
610B SER* 3.2 15.5 + - - +
620B LEU* 3.8 17.4 - - + +
621B GLY* 4.9 3.7 - - - +
631B THR* 3.5 10.2 - - - +
654B ALA 2.9 17.3 + - - +
655B THR 4.0 2.7 - - - +
656B PRO 3.3 0.4 - - - -
657B ALA* 1.3 74.7 - - - +
659B LEU* 1.3 60.8 + - + +
660B VAL 3.3 0.4 + - - -
661B ALA 4.2 8.9 - - - +
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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