Contacts of the helix formed by residues 244 - 258 (chain B) in PDB entry 3MH5
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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B MET* 4.4 14.1 - - - +
153B ALA 2.9 20.7 + - - -
155B SER* 2.6 20.6 + - - -
221B LEU* 3.3 29.3 + - - -
222B ILE* 2.7 22.0 + - - -
223B GLY* 3.7 1.3 - - - -
243B PRO* 1.3 70.9 - - - +
245B ASN* 1.3 49.8 + - - -
247B VAL* 3.0 11.7 + - - +
248B LYS* 2.7 36.5 + - - +
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Residues in contact with ASN 245 (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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153B ALA 3.2 12.5 + - - -
154B ASP* 2.6 25.5 + - - +
155B SER* 2.8 39.5 + - - +
156B ASP* 3.1 18.7 - - - +
243B PRO* 5.9 0.2 - - + -
244B SER* 1.3 71.2 - - - +
246B MET* 1.3 62.8 + - - +
248B LYS* 3.2 18.7 + - - +
249B ASN* 3.0 24.8 + - - +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 5.8 1.6 - - - -
196B GLU* 4.9 22.2 - - + -
197B ASN* 5.1 6.1 - - + +
242B ILE* 3.6 15.9 - - + -
243B PRO* 2.9 31.8 + - + +
245B ASN* 1.3 77.6 - - - +
247B VAL* 1.3 55.8 + - - +
249B ASN* 3.3 32.1 + - + +
250B LEU* 2.9 56.4 + - + +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 5.8 2.0 - - + -
101B VAL* 3.8 31.6 - - + -
136B ILE* 4.4 5.6 - - + -
152B MET* 5.1 8.5 - - - -
221B LEU* 5.1 2.9 - - + -
224B ILE* 3.8 21.1 - - + +
242B ILE* 3.6 26.2 - - + +
243B PRO 2.8 20.8 + - - +
244B SER* 3.3 11.0 - - - +
246B MET* 1.3 74.5 - - - +
248B LYS* 1.3 63.0 + - - +
250B LEU* 4.5 6.7 - - - -
251B THR* 2.8 36.3 + - + +
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Residues in contact with LYS 248 (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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152B MET* 4.3 41.4 + - + +
153B ALA 5.7 1.4 + - - -
244B SER 2.7 15.8 + - - +
245B ASN* 3.2 21.6 + - - +
247B VAL* 1.3 73.0 - - - +
249B ASN* 1.3 64.7 + - - +
251B THR* 3.2 4.9 + - - -
252B SER* 3.1 33.4 + - - +
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Residues in contact with ASN 249 (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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245B ASN 3.0 14.2 + - - +
246B MET* 3.3 29.0 - - + +
248B LYS* 1.3 80.3 - - - +
250B LEU* 1.3 66.5 + - - +
252B SER* 3.3 6.2 + - - -
253B GLN* 3.1 40.3 + - - +
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Residues in contact with LEU 250 (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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131B ASP* 4.0 13.5 - - - +
134B SER* 3.1 30.5 - - - +
136B ILE* 3.9 17.7 - - + -
242B ILE* 4.4 2.5 - - + -
246B MET* 2.9 46.6 + - + +
247B VAL* 3.8 3.4 - - - +
248B LYS 3.3 0.2 - - - -
249B ASN* 1.3 79.0 - - - +
251B THR* 1.3 64.9 + - - +
253B GLN* 2.9 20.0 + - - +
254B MET* 3.0 20.7 + - + +
260B VAL* 3.4 23.0 - - + +
262B ARG* 4.2 11.7 - - - +
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Residues in contact with THR 251 (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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93B ILE* 5.3 11.2 - - + +
101B VAL* 3.9 27.8 - - + -
136B ILE* 4.1 13.2 - - + -
138B LEU* 3.8 29.9 - - + +
152B MET* 5.7 0.5 - - - +
247B VAL* 2.8 26.6 + - + +
248B LYS* 3.2 6.6 + - - -
250B LEU* 1.3 77.1 - - - +
252B SER* 1.3 63.1 + - - +
254B MET* 2.8 29.8 + - + +
255B VAL* 3.0 14.0 + - - +
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Residues in contact with SER 252 (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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248B LYS* 3.1 19.8 + - - +
249B ASN* 3.3 8.5 + - - -
251B THR* 1.3 81.0 + - - +
253B GLN* 1.3 64.8 + - - +
255B VAL* 3.2 20.8 + - - +
256B GLU* 3.2 20.0 + - - +
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Residues in contact with GLN 253 (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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249B ASN* 3.1 34.8 + - - +
250B LEU* 2.9 14.4 + - - +
252B SER* 1.3 81.4 + - - +
254B MET* 1.3 55.5 + - - +
256B GLU* 5.2 0.2 - - - -
257B TYR* 3.0 42.7 + - + -
259B GLN 3.0 12.2 - - - +
260B VAL* 3.2 21.7 - - + +
261B LYS* 2.3 45.9 + - - +
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Residues in contact with MET 254 (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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128B VAL* 4.1 8.7 - - + +
129B GLY* 3.4 40.4 - - - +
130B LYS 3.5 9.6 - - - +
131B ASP* 4.1 9.4 - - + -
136B ILE* 3.5 41.5 - - + +
138B LEU* 3.8 15.5 - - + -
250B LEU* 3.3 22.9 - - + +
251B THR* 2.8 12.0 + - - +
253B GLN* 1.3 76.2 - - - +
255B VAL* 1.3 59.9 + - - +
258B GLY* 2.5 31.7 + - - -
259B GLN* 3.9 11.7 - - - +
260B VAL* 3.8 11.0 - - + +
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Residues in contact with VAL 255 (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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99B TYR* 3.6 44.9 - - + +
128B VAL* 4.6 6.3 - - + -
138B LEU* 3.8 20.0 - - + -
251B THR 3.0 9.2 + - - +
252B SER* 3.4 13.5 - - - +
254B MET* 1.3 79.8 - - - +
256B GLU* 1.3 67.3 + - + +
258B GLY* 4.3 1.4 + - - -
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Residues in contact with GLU 256 (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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252B SER* 3.2 14.8 + - - +
255B VAL* 1.3 86.8 - - + +
257B TYR* 1.3 93.2 + - + +
258B GLY 3.6 0.2 - - - -
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Residues in contact with TYR 257 (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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253B GLN* 3.0 32.0 + - + -
256B GLU* 1.3 105.5 + - + +
258B GLY* 1.3 57.8 + - - +
259B GLN* 2.8 36.5 + - + +
261B LYS* 3.3 44.2 + - + +
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Residues in contact with GLY 258 (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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128B VAL 3.7 19.7 - - - +
129B GLY* 4.1 7.0 - - - -
130B LYS 4.9 1.2 + - - -
254B MET* 2.5 26.2 + - - -
255B VAL 4.3 1.6 + - - -
256B GLU 3.6 1.6 - - - -
257B TYR* 1.3 71.1 - - - +
259B GLN* 1.3 59.9 + - - +
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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