Contacts of the helix formed by residues 1206 - 1210 (chain B) in PDB entry 3DLS
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 LEU1206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A ALA* 4.0 28.0 - - + -
1010A PHE* 3.8 12.1 - - + -
1166B ILE* 3.5 59.2 - - + +
1167B GLU* 4.5 8.5 - - + +
1174B LEU* 3.5 31.1 - - + +
1204B CYS 4.4 0.2 + - - -
1205B GLU* 1.3 73.9 - - - +
1207B GLU* 1.3 58.2 + - - +
1209B THR* 3.2 26.5 - - - -
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Residues in contact with GLU1207 (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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1004A PRO* 3.1 32.1 - - + +
1009A ALA* 4.4 7.4 + - - +
1010A PHE* 3.2 40.5 + - + +
24B MG 2.7 29.1 - - - -
1205B GLU* 3.3 3.6 - - + +
1206B LEU* 1.3 74.8 - - - +
1208B GLU* 1.3 57.7 + - - +
1209B THR 2.8 11.7 + - - -
1210B VAL* 3.2 26.8 + - + +
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Residues in contact with GLU1208 (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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1203B PHE* 3.4 22.1 - - + -
1204B CYS 5.6 0.4 - - - +
1205B GLU* 3.4 26.6 + - + +
1207B GLU* 1.3 75.1 - - - +
1209B THR* 1.3 58.6 + - - +
1210B VAL* 3.6 0.9 - - - -
1211B GLU* 4.5 5.6 - - - +
1212B ALA* 3.6 10.9 + - - -
1213B ALA 4.4 2.6 + - - +
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Residues in contact with THR1209 (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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1169B CYS 4.0 3.9 + - - +
1171B PRO* 3.4 27.5 - - + +
1174B LEU* 3.9 14.7 - - + +
1187B TRP* 3.4 22.2 - - + -
1203B PHE* 3.3 30.7 - - - +
1205B GLU 4.2 0.7 + - - -
1206B LEU* 3.2 20.2 + - - -
1207B GLU 2.8 0.6 + - - -
1208B GLU* 1.3 77.1 - - - +
1210B VAL* 1.3 63.8 + - - +
1211B GLU 3.3 0.7 - - - -
1212B ALA* 3.2 19.5 + - - +
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Residues in contact with VAL1210 (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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1004A PRO* 6.0 1.6 - - + -
1010A PHE* 4.0 17.7 - - + -
1171B PRO* 3.8 21.7 - - + +
1175B MET* 3.7 33.0 - - + -
1207B GLU* 3.4 16.8 - - + +
1209B THR* 1.3 78.1 - - + +
1211B GLU* 1.3 62.1 + - + +
1234B PRO* 3.2 22.0 - - - +
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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