Contacts of the helix formed by residues 1261 - 1266 (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 THR1261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140B PHE* 4.1 2.7 - - - -
1259B ASP 4.4 1.8 + - - -
1260B TYR* 1.3 77.4 + - - +
1262B TRP* 1.3 69.6 + - - +
1263B GLU* 3.9 17.9 - - + +
1264B GLU* 3.1 35.3 + - + +
1265B VAL* 3.0 24.5 + - - +
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Residues in contact with TRP1262 (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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1088B LEU* 3.9 16.2 - - + -
1093B PHE* 3.8 25.1 - + - -
1136B ILE* 4.3 8.1 - - + -
1137B ALA 3.2 23.3 - - - -
1138B GLU* 3.5 42.3 + - + +
1140B PHE* 3.8 36.9 - + - -
1261B THR* 1.3 72.9 - - + +
1263B GLU* 1.3 62.6 + - - +
1265B VAL 3.1 0.9 + - - -
1266B PHE* 2.8 71.5 + + + +
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Residues in contact with GLU1263 (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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1261B THR* 3.3 13.0 - - + +
1262B TRP* 1.3 83.4 - - + +
1264B GLU* 1.3 59.9 + - + +
1266B PHE 3.4 7.0 - - - +
1267B ARG* 3.2 24.4 - - - +
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Residues in contact with GLU1264 (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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1099B ARG* 3.9 8.2 - - - +
1259B ASP 5.4 3.5 - - - +
1260B TYR* 5.8 0.2 - - - -
1261B THR* 3.1 35.7 + - + +
1263B GLU* 1.3 81.2 - - + +
1265B VAL* 1.3 63.6 + - + +
1267B ARG* 3.0 36.2 + - - +
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Residues in contact with VAL1265 (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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1093B PHE* 4.2 8.1 - - + -
1097B HIS 4.6 0.7 - - - +
1098B PRO* 3.4 6.1 - - - +
1099B ARG* 2.8 51.8 + - - +
1100B LEU* 3.9 19.3 - - + -
1104B LEU* 4.0 10.3 - - + -
1140B PHE* 3.6 34.3 - - + -
1260B TYR* 4.3 8.1 - - + -
1261B THR 3.0 22.5 + - - +
1264B GLU* 1.3 82.8 - - + +
1266B PHE* 1.3 60.2 + - - +
1267B ARG* 4.1 2.5 + - - +
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Residues in contact with PHE1266 (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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1088B LEU* 4.0 25.4 - - + -
1093B PHE* 3.3 46.0 - + + -
1096B ARG* 3.3 62.8 - - + -
1098B PRO* 4.7 4.9 - - + -
1262B TRP* 2.8 63.3 + + + +
1263B GLU* 3.4 11.8 - - - +
1265B VAL* 1.3 74.5 - - - +
1267B ARG* 1.3 60.6 + - - +
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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