Contacts of the helix formed by residues 251 - 261 (chain B) in PDB entry 4MCA
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 ALA 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B GLU* 2.8 39.3 + - + +
181B ALA* 4.4 2.7 - - + -
182B CYS* 4.2 4.7 - - - -
250B LEU* 1.3 77.6 - - - +
252B ALA* 1.3 67.4 + - - +
255B ALA* 3.4 5.0 + - - +
282B GLN* 4.2 0.2 - - - +
335B THR* 2.8 37.9 + - - +
338B ASN* 4.5 3.6 - - + -
339B MET* 3.8 19.3 - - - +
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Residues in contact with ALA 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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251B ALA* 1.3 77.9 - - - +
253B ALA* 1.3 67.2 + - - +
255B ALA* 3.2 1.0 + - - -
256B ILE* 2.8 31.2 + - + +
282B GLN* 3.3 17.7 + - + +
285B LEU* 3.9 15.0 - - + -
336B ILE* 3.7 31.6 - - + +
339B MET* 3.9 14.4 - - - -
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Residues in contact with ALA 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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174B SER* 3.9 7.6 - - - -
177B PHE* 6.5 0.2 - - + -
178B GLU* 3.7 14.6 - - + -
251B ALA 3.5 0.6 - - - -
252B ALA* 1.3 75.9 - - - +
254B HIS* 1.3 58.6 + - - +
256B ILE* 3.4 2.3 + - - +
257B HIS* 3.0 25.3 + - - +
275B VAL* 4.3 5.3 - - + +
278B GLY* 3.6 26.3 - - - +
279B THR* 3.6 27.1 - - + +
282B GLN* 2.9 14.3 + - - +
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Residues in contact with HIS 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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140B TYR* 3.8 14.8 - - - +
171B ASP* 3.5 4.3 - - - -
174B SER* 3.4 21.0 + - - -
178B GLU* 2.8 36.5 + - - +
250B LEU* 3.8 13.4 - - + +
253B ALA* 1.3 70.6 - - - +
255B ALA* 1.3 59.8 + - - +
257B HIS* 3.4 6.3 + - - +
258B ASN* 3.0 35.9 + - - +
271B HIS* 3.5 10.5 + + - -
275B VAL* 3.7 10.3 - - + +
335B THR* 4.5 3.4 - - - +
1000B ZN 2.1 36.6 - - - -
1001B GOL 3.0 24.2 + - - -
1004B NA 3.6 8.3 - - - -
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Residues in contact with ALA 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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251B ALA 3.4 11.6 + - - +
252B ALA 3.2 3.4 + - - +
254B HIS* 1.3 77.0 - - - +
256B ILE* 1.3 57.0 + - - +
258B ASN* 3.2 3.6 + - - +
259B GLY 3.0 22.0 + - - -
329B SER* 3.3 33.5 - - - +
334B GLU* 3.6 22.4 - - - +
335B THR* 3.8 1.0 + - - +
336B ILE* 3.6 24.0 - - + +
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Residues in contact with ILE 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 ALA* 2.8 30.7 + - + +
253B ALA 3.9 3.1 - - - +
255B ALA* 1.3 74.8 - - - +
257B HIS* 1.3 66.7 + - - +
259B GLY* 3.1 2.6 + - - -
260B PHE* 2.9 46.7 + - + -
278B GLY* 4.0 20.0 - - - +
281B ALA* 3.9 22.9 - - + -
282B GLN* 4.7 2.5 - - - +
285B LEU* 5.3 3.4 - - + -
325B VAL* 4.2 1.4 - - + +
329B SER* 4.0 8.7 - - - -
336B ILE* 4.3 5.2 - - + -
348B VAL* 3.9 29.4 - - + -
351B ALA* 5.7 1.1 - - + -
352B ILE* 3.9 14.1 - - + -
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Residues in contact with HIS 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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131B TYR* 3.3 25.8 + + - -
253B ALA 3.0 14.7 + - - +
254B HIS* 3.4 8.8 + - - +
256B ILE* 1.3 73.9 - - - +
258B ASN* 1.3 85.6 + - - +
260B PHE* 3.1 20.8 + - - +
261B THR* 3.3 24.2 + - + +
271B HIS* 3.0 47.3 + + - -
274B LYS* 3.8 32.7 + - + -
275B VAL* 3.9 19.5 - - + +
278B GLY* 5.0 1.0 - - - -
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Residues in contact with ASN 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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129B VAL* 5.5 0.7 - - - +
137B PHE* 3.4 45.4 - - + +
140B TYR* 3.3 23.3 + - - -
254B HIS* 3.0 15.5 + - - +
255B ALA 3.5 3.8 - - - +
256B ILE 3.1 0.4 - - - -
257B HIS* 1.3 98.8 + - - +
259B GLY* 1.3 60.0 + - - +
261B THR* 2.6 26.0 + - - -
262B VAL* 4.1 4.3 + - - +
271B HIS* 5.6 0.2 - - - -
328B ALA* 5.0 2.3 - - - +
334B GLU* 3.0 31.4 + - - +
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Residues in contact with GLY 259 (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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255B ALA 3.0 13.4 + - - -
256B ILE 3.1 4.4 + - - -
258B ASN* 1.3 78.1 - - - +
260B PHE* 1.3 54.2 + - - +
262B VAL* 3.1 33.8 + - - +
325B VAL* 3.5 30.9 - - - +
328B ALA* 3.9 11.4 - - - -
329B SER* 4.2 1.9 - - - +
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Residues in contact with PHE 260 (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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256B ILE* 2.9 45.0 + - + -
257B HIS* 3.1 10.7 + - - +
259B GLY* 1.3 69.0 - - - +
261B THR* 1.3 60.7 + - - +
262B VAL 3.1 5.2 - - - -
263B LEU* 3.0 29.1 + - + +
266B CYS* 4.0 28.8 - - - +
274B LYS* 4.5 20.2 - - + -
277B PHE* 4.0 23.6 - + - -
278B GLY 5.5 0.4 - - - -
309B LEU* 3.8 25.8 - - + -
312B MET* 4.6 13.0 - - + -
314B VAL* 4.8 1.1 - - + -
322B ILE* 3.8 20.4 - - + -
325B VAL* 3.7 17.4 - - + +
352B ILE* 4.1 11.0 - - + -
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Residues in contact with THR 261 (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 TYR* 4.1 11.0 - - + -
135B GLY 3.6 12.6 - - - +
136B GLU* 3.2 13.5 - - - +
137B PHE 2.8 26.0 + - - -
257B HIS* 3.3 36.5 + - + +
258B ASN* 2.6 20.3 + - - +
259B GLY 3.2 0.4 - - - -
260B PHE* 1.3 76.2 - - - +
262B VAL* 1.3 59.5 + - - +
263B LEU 3.2 0.4 - - - -
267B HIS* 3.0 29.4 + - + +
274B LYS* 5.3 8.7 - - - +
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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