Contacts of the helix formed by residues 255 - 261 (chain A) in PDB entry 1TQ6
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 LYS 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A SER* 3.3 17.2 + - - +
69A VAL 3.2 27.2 + - - +
70A LEU* 3.9 13.7 - - + +
150A ASP* 2.9 25.6 + - - +
251A LEU* 4.0 13.7 - - + +
252A PRO* 3.0 34.3 + - + +
254A TYR* 1.3 109.0 + - + +
256A ARG* 1.3 64.8 + - - +
257A HIS 3.4 1.7 + - - -
258A ASN* 3.7 6.3 + - - +
259A PHE* 3.5 19.9 + - - +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR 4.7 2.6 + - - -
30A GLY* 3.4 32.7 + - - -
32A LYS 4.7 8.9 + - - +
33A ILE* 6.0 0.2 - - - -
248A ILE* 3.2 33.5 + - + +
249A SER* 3.0 30.7 + - - +
251A LEU* 3.1 30.0 + - + -
252A PRO 3.7 5.2 - - - +
253A ILE* 3.2 37.3 + - - +
255A LYS* 1.3 76.5 - - - +
257A HIS* 1.3 55.7 + - - +
259A PHE* 3.7 0.7 - - - +
260A MET* 2.7 37.9 + - - +
277A PHE* 3.9 17.9 - - + -
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Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.5 23.7 - - + +
65A ILE* 3.6 28.4 - - + +
66A ASP* 4.6 3.8 - - - -
253A ILE 4.5 2.0 + - - +
254A TYR 4.7 2.8 + - - +
255A LYS 3.4 0.8 - - - -
256A ARG* 1.3 78.0 - - - +
258A ASN* 1.3 81.9 + - - +
260A MET* 3.7 0.3 - - - +
261A VAL* 3.1 39.8 + - + +
277A PHE* 3.9 24.2 - + + -
278A LEU* 3.7 26.8 - - + +
281A ARG* 3.7 23.6 + - + -
315A PHE* 5.0 8.7 - + - -
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE 3.0 17.0 + - - +
66A ASP* 2.9 32.1 + - - +
68A SER* 3.1 18.4 - - - +
70A LEU* 6.0 2.9 - - + -
119A ILE* 3.7 24.1 - - + +
121A ASN* 4.3 3.1 - - + +
122A VAL* 3.8 6.2 - - + +
255A LYS 3.7 8.1 + - - +
256A ARG 3.4 0.8 - - - -
257A HIS* 1.3 102.7 + - - +
259A PHE* 1.3 62.4 + - - +
261A VAL* 3.3 18.4 - - - +
262A SER* 3.4 12.1 + - - -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.3 30.3 - - + -
72A VAL* 4.8 5.2 - - + -
89A LEU* 5.2 4.3 - - + -
122A VAL* 4.2 16.8 - - + +
124A PHE* 4.6 14.1 - + - -
151A PHE* 4.0 9.9 - + - -
244A MET 5.1 0.4 - - - -
247A LEU* 3.8 39.0 - - + -
248A ILE* 3.3 23.3 - - + -
251A LEU* 4.0 13.0 - - + -
255A LYS 3.5 10.1 + - - +
256A ARG 3.3 3.2 + - - +
258A ASN* 1.3 77.1 - - - +
260A MET* 1.3 64.9 + - - +
262A SER* 2.5 27.1 + - - -
263A LEU* 3.1 41.3 - - + +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 4.0 11.8 - - + +
256A ARG 2.7 25.1 + - - +
257A HIS 3.7 3.6 - - - +
259A PHE* 1.3 75.9 - - - +
261A VAL* 1.3 63.4 + - + +
262A SER 3.1 0.9 + - - -
263A LEU* 3.3 33.0 + - + +
270A VAL* 3.8 33.4 - - + +
273A LYS* 3.6 37.9 - - + -
274A LYS* 3.2 26.2 - - + -
277A PHE* 3.8 30.7 - - + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 5.4 0.9 - - - -
119A ILE* 3.6 24.8 - - + +
257A HIS* 3.1 43.4 + - + +
258A ASN* 3.3 16.2 - - - +
260A MET* 1.3 77.6 - - + +
262A SER* 1.3 60.1 + - - +
274A LYS* 3.4 26.6 + - + +
277A PHE* 5.3 2.5 - - + -
278A LEU* 4.3 18.8 - - + -
315A PHE* 5.0 4.3 - - + -
319A VAL* 3.7 29.6 - - + +
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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