Contacts of the helix formed by residues 670 - 678 (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 GLY 670 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669B TYR* 1.3 79.2 - - - +
671B PRO* 1.3 78.5 - - - +
672B SER 3.1 3.7 + - - -
673B ALA* 3.2 5.1 + - - +
674B THR* 2.8 21.0 + - - -
690B SER* 3.3 11.7 - - - -
692B THR* 4.8 0.4 - - - -
710B THR* 4.0 12.0 - - - +
713B GLU* 3.6 7.4 + - - -
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Residues in contact with PRO 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B GLY* 1.3 83.2 - - - +
672B SER* 1.3 62.5 + - - +
674B THR* 3.8 4.7 - - - +
675B SER* 2.9 31.9 + - - +
684B GLU* 6.0 0.4 - - - +
690B SER* 3.6 6.0 - - - +
693B GLU* 3.6 26.2 - - - +
713B GLU* 2.9 16.6 - - + +
714B THR 3.7 22.2 - - - +
715B ALA* 4.5 2.5 - - - -
716B THR* 3.7 26.7 - - + +
725B LEU* 4.1 15.0 - - + -
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B PRO* 1.3 78.1 - - - +
673B ALA* 1.3 62.5 + - - +
675B SER* 3.6 9.5 + - - -
676B GLU* 3.6 13.9 + - - +
713B GLU* 2.8 33.7 + - - -
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Residues in contact with ALA 673 (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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667B LYS 3.6 24.7 - - - +
668B CYS* 4.3 1.1 - - - -
669B TYR* 4.3 6.7 - - + +
670B GLY 3.2 8.8 + - - +
672B SER* 1.3 81.6 + - - +
674B THR* 1.3 51.7 + - - +
676B GLU* 3.3 4.2 + - - +
677B LYS* 2.5 53.7 + - + +
713B GLU* 5.9 0.2 - - - +
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Residues in contact with THR 674 (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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668B CYS* 3.5 14.6 + - + +
670B GLY 2.8 21.2 + - - -
671B PRO* 3.8 4.3 - - - -
673B ALA* 1.3 72.9 - - - +
675B SER* 1.3 64.4 + - - +
676B GLU 3.0 1.8 - - - -
678B CYS* 2.6 58.9 + - + +
681B ASN* 3.9 8.5 - - + +
682B ALA* 3.6 21.5 - - - +
690B SER* 2.9 29.2 - - - +
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Residues in contact with SER 675 (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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671B PRO* 2.9 18.9 + - - +
672B SER* 3.9 5.1 - - - -
674B THR* 1.3 76.8 - - - +
676B GLU* 1.3 60.0 + - - +
679B PRO* 3.8 10.2 - - - +
682B ALA* 3.8 12.1 - - - +
684B GLU* 2.6 29.8 + - - -
685B LYS* 3.6 17.9 + - - +
716B THR* 4.5 5.9 - - - +
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Residues in contact with GLU 676 (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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672B SER 3.6 10.5 + - - +
673B ALA* 3.5 8.0 - - - +
674B THR 3.0 0.4 - - - -
675B SER* 1.3 82.2 - - - +
677B LYS* 1.3 88.2 + - + +
678B CYS 3.7 0.2 - - - -
679B PRO* 3.9 9.5 - - - +
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Residues in contact with LYS 677 (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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664B THR* 4.5 3.1 + - - -
665B SER* 4.8 11.6 - - - +
667B LYS* 3.8 34.7 - - + +
668B CYS* 3.7 11.4 - - - -
673B ALA* 2.5 40.5 + - + +
676B GLU* 1.3 95.9 - - + +
678B CYS* 1.3 61.4 + - - +
679B PRO* 3.3 11.1 - - - +
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Residues in contact with CYS 678 (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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663B VAL* 4.3 0.9 - - - -
664B THR* 3.8 9.2 - - - +
665B SER* 3.6 29.4 - - - -
668B CYS* 2.0 46.5 - - - -
674B THR* 2.6 21.7 + - + +
677B LYS* 1.3 75.8 - - - +
679B PRO* 1.3 58.1 - - - +
680B GLY 3.2 2.7 - - - -
681B ASN* 2.7 41.9 + - + +
682B ALA 3.0 8.5 + - - -
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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