Contacts of the helix formed by residues 251 - 268 (chain A) in PDB entry 5T0I
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 GLY 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A VAL* 1.3 74.5 - - - +
252A GLU* 1.3 63.2 + - - +
253A GLY 3.3 2.8 - - - +
254A ALA* 3.5 13.1 + - - +
255A ARG* 3.0 34.2 + - - +
301A GLU* 4.8 9.9 + - - -
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Residues in contact with GLU 252 (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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158A ASP* 4.3 17.2 - - - +
159A PRO* 4.7 5.9 - - - +
160A THR* 5.1 1.9 + - - -
161A VAL* 3.4 30.6 - - + +
244A GLU 5.4 1.6 - - - +
245A LEU* 5.5 10.3 - - + +
248A LYS* 4.9 8.0 - - - -
249A TYR* 3.1 53.2 + - + +
250A VAL 3.4 1.2 - - - +
251A GLY* 1.3 77.7 - - - +
253A GLY* 1.3 53.6 + - - +
255A ARG* 3.0 19.4 + - - +
256A MET* 2.4 43.9 + - + +
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Residues in contact with GLY 253 (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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245A LEU* 4.1 27.6 + - - +
251A GLY* 3.3 1.6 - - - +
252A GLU* 1.3 78.0 - - - +
254A ALA* 1.3 60.3 + - - +
256A MET* 3.7 4.7 - - - +
257A VAL* 3.0 28.0 + - - +
301A GLU* 5.5 2.0 - - - -
302A LEU* 6.0 1.4 - - - +
305A GLN* 5.6 0.7 - - - -
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Residues in contact with ALA 254 (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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251A GLY* 3.5 11.4 + - - +
252A GLU 3.3 0.6 - - - -
253A GLY* 1.3 72.1 - - - +
255A ARG* 1.3 68.3 + - + +
256A MET 3.1 0.5 + - - -
257A VAL* 3.2 7.6 + - - +
258A ARG* 3.1 34.7 + - - +
301A GLU* 3.2 31.6 + - + +
305A GLN* 4.3 13.0 - - - +
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Residues in contact with ARG 255 (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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157A ILE* 3.6 24.3 - - + +
158A ASP* 3.0 26.4 + - - +
159A PRO* 4.7 6.9 - - - +
249A TYR* 5.9 3.8 - - - -
250A VAL 5.7 1.6 + - - -
251A GLY* 3.0 18.2 + - - +
252A GLU* 3.0 19.9 + - - +
254A ALA* 1.3 79.2 - - + +
256A MET* 1.3 59.4 + - - +
258A ARG* 3.5 17.0 + - - +
259A GLU* 2.7 37.6 + - - +
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Residues in contact with MET 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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161A VAL* 3.7 35.4 - - + +
165A GLN* 3.4 46.4 - - + +
240A VAL* 4.5 10.1 - - - -
245A LEU* 4.1 35.2 - - + -
252A GLU* 2.4 35.9 + - + +
253A GLY 3.7 3.8 - - - +
255A ARG* 1.3 68.8 - - - +
257A VAL* 1.3 62.5 + - + +
259A GLU* 3.2 18.4 + - - +
260A LEU* 3.1 30.6 + - + +
274A PHE* 5.6 3.1 - - - -
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Residues in contact with VAL 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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253A GLY 3.0 16.9 + - - +
254A ALA 3.2 14.1 - - - +
256A MET* 1.3 75.8 - - + +
258A ARG* 1.3 59.3 + - - +
260A LEU* 3.3 19.6 - - + +
261A PHE* 3.2 40.1 - - + -
272A ILE* 5.5 0.4 - - + -
274A PHE* 5.0 17.3 - - + -
302A LEU* 5.2 4.0 - - + -
305A GLN* 3.4 42.2 - - + +
306A LEU* 5.0 4.7 - - + -
312A ARG* 4.4 8.7 - - - +
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Residues in contact with ARG 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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254A ALA* 3.1 26.1 + - - +
255A ARG* 3.9 13.8 - - - +
256A MET 3.1 0.6 - - - -
257A VAL* 1.3 79.8 - - - +
259A GLU* 1.3 61.3 + - - +
261A PHE* 3.7 3.3 + - - +
262A GLU* 3.3 20.4 + - - +
305A GLN* 3.5 21.8 - - - +
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Residues in contact with GLU 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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157A ILE* 3.1 43.6 - - + +
158A ASP* 4.3 9.4 - - - +
161A VAL* 5.4 2.6 - - - +
162A THR* 6.0 1.0 - - - +
165A GLN* 4.9 4.1 + - - +
255A ARG* 2.7 22.9 + - - +
256A MET* 3.2 23.8 + - + +
258A ARG* 1.3 78.9 - - - +
260A LEU* 1.3 59.7 + - + +
262A GLU* 3.1 7.0 + - - +
263A MET* 2.6 53.4 + - + +
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Residues in contact with LEU 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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165A GLN* 3.4 29.4 - - - +
238A ILE* 5.1 4.5 - - + -
240A VAL* 5.4 1.3 - - + -
256A MET* 3.1 23.6 + - + +
257A VAL* 3.3 25.4 - - + +
259A GLU* 1.3 79.3 - - + +
261A PHE* 1.3 95.7 + - + +
263A MET* 3.8 10.4 - - - +
264A ALA* 2.8 24.9 + - - +
270A CYS* 5.5 4.2 - - - -
272A ILE* 3.6 42.1 - - + +
274A PHE* 5.6 2.0 - - + -
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Residues in contact with PHE 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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257A VAL* 3.2 28.5 - - + +
258A ARG 3.7 3.9 + - - +
259A GLU 3.2 0.4 - - - -
260A LEU* 1.3 87.2 - - + +
262A GLU* 1.3 61.9 + - - +
263A MET 3.3 0.2 - - - -
264A ALA* 3.3 10.0 - - + +
265A ARG* 2.8 54.4 + - + +
272A ILE* 3.6 22.7 - - + -
305A GLN 5.3 0.4 - - - -
310A ASP 4.7 5.6 - - - +
311A PRO* 6.2 2.0 - - + -
312A ARG* 3.2 54.1 - - - -
313A GLY* 4.9 6.3 - - - -
314A ASN 5.7 1.6 - - - -
315A ILE* 4.1 16.8 - - + -
317A VAL* 3.9 7.4 - - + -
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Residues in contact with GLU 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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258A ARG 3.3 13.4 + - - +
259A GLU* 3.1 10.9 + - - +
261A PHE* 1.3 80.2 - - - +
263A MET* 1.3 60.5 + - + +
265A ARG* 3.6 33.5 + - - +
266A THR* 3.6 15.2 + - - -
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Residues in contact with MET 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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157A ILE* 6.4 0.9 - - - -
259A GLU* 2.6 38.0 + - + +
260A LEU* 3.8 9.6 - - - +
262A GLU* 1.3 71.4 - - + +
264A ALA* 1.3 68.4 + - - +
266A THR* 3.6 14.7 + - - -
267A LYS* 3.8 10.0 + - - +
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Residues in contact with ALA 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 LEU 2.8 20.8 + - - +
261A PHE* 3.2 19.3 + - + +
263A MET* 1.3 74.7 - - - +
265A ARG* 1.3 52.3 + - + +
266A THR 2.7 8.5 + - - -
267A LYS* 2.7 4.6 + - - -
268A LYS* 2.3 49.4 + - - +
270A CYS* 4.6 19.3 - - + +
314A ASN* 5.7 4.9 - - + +
315A ILE* 6.0 1.1 - - + -
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Residues in contact with ARG 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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261A PHE* 2.8 37.0 + - + +
262A GLU* 3.6 26.3 + - - +
263A MET 3.5 0.6 - - - -
264A ALA* 1.3 71.3 - - + +
266A THR* 1.3 64.3 + - - +
268A LYS* 3.9 18.8 + - - +
310A ASP* 3.3 40.2 + - - +
311A PRO* 4.8 10.1 - - + +
314A ASN* 4.1 17.3 - - - +
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Residues in contact with THR 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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262A GLU 3.6 13.4 + - - -
263A MET* 3.7 9.0 + - - -
264A ALA 2.7 4.6 + - - -
265A ARG* 1.3 78.9 - - - +
267A LYS* 1.3 86.8 + - + +
268A LYS* 5.2 2.9 - - - +
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Residues in contact with LYS 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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263A MET 4.3 8.0 + - - +
264A ALA 2.7 5.0 + - - +
266A THR* 1.3 102.8 - - + +
268A LYS* 1.3 78.0 + - - +
269A ALA* 3.6 8.4 + - + +
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Residues in contact with LYS 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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195A LEU* 5.7 9.9 - - + +
198A PRO* 6.2 1.6 - - - +
264A ALA* 2.3 35.4 + - - +
265A ARG* 4.0 17.3 - - - +
266A THR 3.4 2.6 - - - -
267A LYS* 1.3 82.2 + - - +
269A ALA* 1.3 70.7 + - + +
270A CYS* 2.9 11.9 + - - +
314A ASN* 4.7 24.0 - - + +
315A ILE* 5.4 0.2 - - - -
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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