Contacts of the helix formed by residues 258 - 267 (chain A) in PDB entry 5THH
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 ASN 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A PRO* 4.6 1.9 - - - +
249A PHE* 4.4 5.5 - - - +
250A CYS* 3.7 24.3 - - - +
251A GLU 4.5 1.4 + - - +
254A ASN* 3.0 28.7 + - + +
255A VAL 4.4 2.4 + - - +
256A GLU 2.8 7.3 + - - +
257A ASN* 1.3 72.5 - - - +
259A GLY* 1.3 56.0 + - - +
260A VAL* 3.1 12.8 + - - +
261A LEU* 3.0 36.2 + - + +
262A SER* 2.9 31.6 + - - -
299A PHE* 3.6 18.4 - - - -
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Residues in contact with GLY 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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216A PRO* 3.9 18.4 - - - +
217A GLY 3.3 25.6 - - - -
218A LEU* 3.7 8.4 + - - +
249A PHE* 4.3 7.5 + - - -
257A ASN 3.8 4.4 + - - -
258A ASN* 1.3 71.4 + - - +
260A VAL* 1.3 59.1 + - - +
262A SER* 3.8 2.6 - - - -
263A PHE* 3.0 28.6 + - - +
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Residues in contact with VAL 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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218A LEU* 3.8 18.6 - - + +
245A LEU* 5.1 1.6 - - + -
248A ALA* 4.5 15.3 - - + -
249A PHE 4.6 2.7 - - - +
250A CYS* 4.1 18.8 - - + -
258A ASN* 3.1 8.7 + - - +
259A GLY* 1.3 75.8 - - - +
261A LEU* 1.3 66.9 + - - +
263A PHE* 3.2 4.2 + - - +
264A ILE* 3.0 25.0 + - - +
309A LEU* 3.7 29.4 - - + +
310A LYS* 4.4 14.1 - - + +
313A VAL* 3.6 29.1 - - + +
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Residues in contact with LEU 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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255A VAL* 3.7 33.4 - - + +
258A ASN* 3.0 37.6 + - + +
260A VAL* 1.3 76.4 - - - +
262A SER* 1.3 57.4 + - - +
264A ILE* 3.1 7.1 + - + +
265A LYS* 2.9 29.5 + - - +
292A TYR* 3.4 25.8 - - + +
295A LEU* 4.1 30.3 - - + -
296A GLU* 5.2 2.5 - - - -
299A PHE* 3.8 20.0 - - + -
309A LEU* 4.0 20.4 - - + -
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Residues in contact with SER 262 (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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215A VAL* 3.6 24.6 - - - +
216A PRO* 3.5 20.9 - - - +
258A ASN 2.9 18.9 + - - -
259A GLY* 3.8 6.1 - - - -
260A VAL 3.2 0.2 - - - -
261A LEU* 1.3 73.5 - - - +
263A PHE* 1.3 61.3 - - - +
265A LYS* 3.3 6.6 + - - -
266A HIS* 2.9 41.7 + - - +
292A TYR* 5.4 0.2 - - - -
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Residues in contact with PHE 263 (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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50A VAL* 3.9 24.0 - - + -
51A ALA* 5.3 2.7 - - - -
53A PHE* 4.1 8.1 - + + -
54A VAL* 5.1 6.1 - - + -
215A VAL* 5.0 3.1 - - - +
218A LEU* 3.8 31.4 - - + -
259A GLY 3.0 18.8 + - - +
260A VAL 3.2 4.5 + - - +
262A SER* 1.3 74.7 - - - +
264A ILE* 1.3 64.9 + - + +
266A HIS* 5.2 0.7 - - - -
267A VAL* 2.9 65.9 + - + +
268A LEU* 3.4 26.2 + - + -
313A VAL* 4.3 11.2 - - + -
317A LEU* 4.0 31.9 - - + -
320A LEU* 4.8 1.6 - - + -
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Residues in contact with ILE 264 (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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260A VAL 3.0 16.2 + - - +
261A LEU* 3.4 8.5 - - - +
263A PHE* 1.3 77.3 - - - +
265A LYS* 1.3 63.7 + - - +
268A LEU* 3.2 10.3 + - + -
269A PHE* 3.0 52.8 + - + -
275A PHE* 3.7 28.3 - - + -
292A TYR* 4.5 0.9 - - + -
295A LEU* 3.8 14.6 - - + -
309A LEU* 3.5 30.7 - - + -
313A VAL* 3.5 31.6 - - + -
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Residues in contact with LYS 265 (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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17A ASN* 3.6 25.2 + - - +
261A LEU 2.9 19.5 + - - +
262A SER* 3.3 6.9 + - - +
264A ILE* 1.3 75.1 - - - +
266A HIS* 1.3 80.4 + - + +
269A PHE* 4.2 5.2 - - - +
270A PRO* 3.3 16.8 - - - +
292A TYR* 3.6 50.5 - - + -
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Residues in contact with HIS 266 (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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17A ASN* 3.6 33.1 + - + +
54A VAL* 4.3 25.1 - - + +
57A SER* 3.3 21.1 - - - -
212A ASN* 4.8 4.9 + - - -
213A PRO* 3.5 33.2 - - + +
215A VAL* 3.9 18.5 - - + +
262A SER* 2.9 35.1 + - - +
265A LYS* 1.3 99.7 + - + +
267A VAL* 1.3 61.2 + - - +
270A PRO* 3.5 9.7 - - - +
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Residues in contact with VAL 267 (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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53A PHE* 3.6 45.1 - - + +
54A VAL* 3.8 15.5 - - + -
57A SER* 3.5 14.0 + - - +
108A ILE* 5.3 4.5 - - + -
263A PHE* 2.9 37.4 + - + +
265A LYS 3.5 0.2 - - - -
266A HIS* 1.3 86.7 - - - +
268A LEU* 1.3 70.7 + - + +
269A PHE 3.5 1.3 - - - -
270A PRO* 3.6 1.7 - - - +
271A LEU* 3.2 23.1 + - + +
320A LEU* 4.2 9.6 - - + -
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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