Contacts of the helix formed by residues 1248 - 1253 (chain E) 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 ASP1248 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223E GLU 4.7 1.7 - - - +
1227E LEU* 3.7 30.8 - - - +
1240E THR* 6.0 1.7 - - - +
1244E LYS 3.1 13.6 + - - +
1245E LEU* 3.2 19.8 + - - +
1246E VAL 3.4 0.4 - - - -
1247E THR* 1.3 77.8 - - - +
1249E PRO* 1.4 71.6 - - - +
1250E TRP* 3.2 33.1 + - - +
1251E VAL* 3.0 25.7 + - + +
1252E THR* 3.1 12.0 + - - -
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Residues in contact with PRO1249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223E GLU* 5.4 11.9 - - + -
1247E THR 3.4 6.0 - - - +
1248E ASP* 1.4 95.7 - - - +
1250E TRP* 1.3 54.6 + - - +
1252E THR* 3.9 2.1 - - - +
1253E GLN* 3.1 30.8 + - - +
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Residues in contact with TRP1250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102E GLU* 2.9 54.9 + - + +
1105E ALA* 4.0 9.9 - - + -
1106E SER* 2.7 52.3 + - - -
1109E PHE* 4.1 10.1 - + + -
1193E LEU* 3.6 31.9 - - + -
1197E VAL* 4.3 1.3 - - + -
1221E SER* 4.0 7.0 - - - -
1223E GLU* 4.3 19.3 - - + +
1224E LEU* 3.5 35.8 - - + +
1227E LEU* 3.5 20.0 - - + -
1248E ASP* 3.2 12.0 + - - +
1249E PRO* 1.3 78.5 - - - +
1251E VAL* 1.3 55.7 + - + +
1253E GLN* 2.9 27.7 + - - +
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Residues in contact with VAL1251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106E SER* 3.4 3.7 + - - -
1109E PHE* 4.1 11.7 - - + -
1110E ARG* 2.9 50.9 + - + +
1113E VAL* 4.8 9.4 - - + -
1227E LEU* 3.8 16.4 - - + -
1245E LEU* 3.6 41.5 - - + +
1246E VAL* 4.2 12.1 - - - +
1248E ASP* 3.0 16.8 + - + +
1250E TRP* 1.3 80.2 - - + +
1252E THR* 1.3 58.7 + - - +
1253E GLN 3.5 0.2 - - - -
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Residues in contact with THR1252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110E ARG* 3.8 9.2 + - - +
1246E VAL 4.7 11.0 - - - -
1247E THR* 5.2 4.5 - - - -
1248E ASP 3.1 11.8 + - - -
1249E PRO* 3.9 2.5 - - - -
1251E VAL* 1.3 75.5 - - - +
1253E GLN* 1.3 66.8 + - - +
1254E PRO* 3.9 0.7 - - - +
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Residues in contact with GLN1253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102E GLU* 4.0 2.2 - - - +
1103E PRO* 3.1 43.4 - - + +
1106E SER* 3.9 5.4 - - - -
1110E ARG* 2.8 38.3 + - - +
1249E PRO 3.1 15.0 + - - +
1250E TRP* 2.9 45.9 - - - +
1251E VAL 3.5 0.2 - - - -
1252E THR* 1.3 77.8 - - - +
1254E PRO* 1.4 75.0 + - + +
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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