Contacts of the helix formed by residues 259 - 272 (chain A) in PDB entry 5TQB
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 SER 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.3 6.1 - - - -
21A GLU* 4.2 17.4 - - - -
152A VAL* 3.8 17.5 - - - -
153A VAL 2.7 14.8 + - - -
154A ASP* 3.6 9.9 + - - -
155A SER* 2.6 38.6 + - - -
258A THR* 1.3 71.6 - - - +
260A ALA* 1.3 59.9 + - - +
261A ALA 3.3 0.3 + - - -
262A ILE* 3.4 11.1 + - - +
263A LYS* 3.5 18.6 + - - +
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Residues in contact with ALA 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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155A SER* 2.8 21.5 + - - +
214A SER* 3.8 14.6 - - - +
217A HIS* 4.1 17.2 - - + -
218A ASP* 3.4 15.5 - - - +
259A SER* 1.3 77.4 + - - +
261A ALA* 1.3 61.7 + - - +
263A LYS* 3.7 7.0 + - - +
264A GLN* 3.5 27.0 + - - +
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Residues in contact with ALA 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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212A VAL 3.6 14.8 - - - +
214A SER* 3.9 4.5 - - - +
237A VAL* 3.3 33.6 - - + +
257A TRP* 4.1 10.5 - - + -
258A THR* 2.8 23.9 + - - +
260A ALA* 1.3 78.2 - - - +
262A ILE* 1.3 59.6 + - - +
264A GLN* 3.4 2.4 + - - +
265A LEU* 2.8 31.3 + - - +
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Residues in contact with ILE 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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7A VAL* 5.0 3.8 - - + -
21A GLU* 4.2 16.2 - - + +
22A VAL 3.9 10.5 - - - +
24A PRO* 3.8 28.3 - - + +
27A PHE* 4.3 18.4 - - + -
150A PRO* 5.0 2.5 - - + -
152A VAL* 3.8 21.1 - - + -
257A TRP* 3.6 49.4 - - + -
258A THR 3.1 6.3 + - - +
259A SER* 3.8 9.0 - - - +
261A ALA* 1.3 78.9 - - - +
263A LYS* 1.3 65.9 + - - +
265A LEU* 3.2 18.0 + - + +
266A ASP 4.1 1.2 + - - -
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Residues in contact with LYS 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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21A GLU* 2.9 40.4 + - - +
259A SER 3.5 10.6 + - - +
260A ALA* 3.9 9.9 - - - +
261A ALA 3.3 0.6 - - - -
262A ILE* 1.3 83.6 - - + +
264A GLN* 1.3 64.2 + - + +
265A LEU 3.4 0.2 + - - -
266A ASP* 3.9 10.7 + - - +
267A ALA* 4.5 2.8 + - - +
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Residues in contact with GLN 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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214A SER* 2.5 38.1 + - - +
215A PRO* 5.0 3.4 - - - +
216A GLU* 3.5 12.9 - - - +
217A HIS* 3.4 22.6 + - + +
237A VAL* 4.6 9.2 - - + +
260A ALA 3.5 8.2 + - - +
261A ALA 3.4 5.1 + - - +
262A ILE 3.4 0.4 - - - -
263A LYS* 1.3 77.4 - - + +
265A LEU* 1.3 56.8 + - - +
267A ALA* 2.7 32.2 + - + +
268A VAL* 2.9 25.4 + - + +
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Residues in contact with LEU 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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24A PRO* 4.0 14.4 - - + -
26A VAL* 3.3 34.8 - - + -
27A PHE* 4.6 2.5 - - + -
127A LEU* 4.5 11.0 - - + -
237A VAL* 3.7 20.6 - - + +
240A LEU* 4.2 10.5 - - + -
257A TRP* 3.6 34.1 - - + -
261A ALA 2.8 15.3 + - - +
262A ILE* 3.2 17.0 - - - +
263A LYS 3.2 0.6 - - - -
264A GLN* 1.3 76.6 - - - +
266A ASP* 1.3 61.5 + - - +
268A VAL* 4.0 3.0 - - + +
269A TYR* 3.4 22.0 + - + +
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Residues in contact with ASP 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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24A PRO* 3.8 12.7 - - + +
25A LYS* 3.3 44.7 + - - +
26A VAL* 3.6 14.6 + - - +
262A ILE 4.1 0.8 + - - -
263A LYS 3.9 8.4 + - - +
264A GLN 2.9 1.4 + - - -
265A LEU* 1.3 81.5 - - - +
267A ALA* 1.3 59.6 + - - +
269A TYR* 4.0 4.5 + - - +
270A GLU* 3.1 44.9 + - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LYS 4.5 1.9 + - - +
264A GLN* 2.7 20.9 + - + +
266A ASP* 1.3 74.4 - - - +
268A VAL* 1.3 60.2 + - + +
270A GLU* 3.2 12.0 + - - +
271A SER* 2.9 28.7 + - - -
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Residues in contact with VAL 268 (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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237A VAL* 4.1 17.7 - - + +
238A ASP* 3.7 35.9 - - + +
264A GLN* 2.9 33.9 + - + +
265A LEU* 4.0 7.4 - - + +
266A ASP 3.5 0.2 - - - -
267A ALA* 1.3 77.5 - - + +
269A TYR* 1.3 63.6 + - - +
271A SER* 3.1 22.1 + - - -
272A LYS* 3.4 17.4 + - + +
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Residues in contact with TYR 269 (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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26A VAL* 4.3 21.5 - - + -
120A ARG* 2.9 47.4 + - + +
121A PHE* 4.0 3.6 - - - -
123A THR* 4.2 16.4 - - + -
124A ALA* 3.3 30.9 - - + +
127A LEU* 5.0 6.5 - - + -
265A LEU* 3.4 16.0 + - + +
266A ASP* 4.4 4.5 - - - +
267A ALA 3.4 0.2 - - - -
268A VAL* 1.3 81.5 - - - +
270A GLU* 1.3 69.2 + - + +
271A SER 3.6 0.2 + - - -
272A LYS* 3.8 17.5 + - + +
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Residues in contact with GLU 270 (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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25A LYS* 5.5 4.5 - - - +
266A ASP* 3.1 33.8 + - - +
267A ALA* 3.2 12.6 + - - +
268A VAL 3.2 0.4 - - - -
269A TYR* 1.3 83.9 - - + +
271A SER* 1.3 64.6 + - - +
272A LYS 3.4 3.7 - - - -
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Residues in contact with SER 271 (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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267A ALA 2.9 13.5 + - - -
268A VAL* 3.1 15.2 + - - -
270A GLU* 1.3 79.2 - - - +
272A LYS* 1.3 70.7 + - - +
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Residues in contact with LYS 272 (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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120A ARG* 4.1 25.8 + - - +
238A ASP* 5.2 13.7 - - - +
268A VAL* 3.4 19.8 + - + +
269A TYR* 3.8 13.1 + - + +
270A GLU 3.4 3.7 - - - -
271A SER* 1.3 89.4 + - - +
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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