Contacts of the helix formed by residues 271 - 278 (chain B) in PDB entry 3A7H
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 HIS 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B PRO* 3.4 27.6 - - + -
249B GLU* 4.1 12.6 + - + +
250B PHE* 3.7 36.7 + + + -
253B ALA* 4.9 6.3 - - + +
267B GLU 3.5 3.7 + - - +
268B LEU* 2.9 32.0 + - + +
270B LYS* 1.3 81.4 - - - +
272B LYS* 1.3 72.4 + - + +
273B PHE* 3.1 27.1 + - - +
274B ILE* 3.0 15.3 + - + +
275B LEU* 3.1 9.2 + - - +
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Residues in contact with LYS 272 (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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47A GLN* 6.3 1.0 - - - +
245B LYS* 6.2 0.4 - - - +
246B PRO* 3.7 23.2 - - + +
249B GLU* 4.1 17.7 + - - +
270B LYS 3.3 4.6 + - - -
271B HIS* 1.3 79.3 + - + +
273B PHE* 1.3 67.7 + - - +
275B LEU* 3.9 8.7 - - - -
276B ARG* 3.0 73.0 + - + +
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Residues in contact with PHE 273 (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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118B GLU* 3.4 46.7 - - + -
121B ILE* 4.0 9.9 - - + -
122B ALA* 3.6 23.6 - - + -
125B LEU* 4.1 5.2 - - + -
244B SER* 4.3 2.0 - - - -
246B PRO* 3.5 24.5 - - + +
247B LEU* 3.6 42.8 - - + -
250B PHE* 4.1 12.6 - + + -
271B HIS* 3.1 12.9 + - - +
272B LYS* 1.3 79.3 - - - +
274B ILE* 1.3 72.7 + - + +
276B ARG* 4.9 0.2 - - - -
277B ASN* 2.8 49.3 + - - +
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Residues in contact with ILE 274 (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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122B ALA* 3.4 26.0 - - - +
125B LEU* 4.0 12.3 - - + -
126B ARG* 3.8 44.0 - - + +
129B LEU* 4.2 7.2 - - + -
250B PHE* 4.0 14.8 - - + -
268B LEU 3.6 17.3 - - - +
269B LEU* 3.6 20.2 - - - +
271B HIS 3.0 7.9 + - - +
273B PHE* 1.3 83.7 - - + +
275B LEU* 1.3 64.4 + - + +
278B ALA* 2.9 37.3 + - + +
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Residues in contact with LEU 275 (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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269B LEU 3.7 17.3 - - - +
270B LYS* 3.6 25.1 - - + +
271B HIS 3.1 14.3 + - - +
272B LYS* 3.5 7.6 + - + +
274B ILE* 1.3 80.1 - - + +
276B ARG* 1.3 61.3 + - + +
277B ASN 3.8 0.2 + - - -
278B ALA 4.8 4.5 + - - +
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Residues in contact with ARG 276 (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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45A ARG 3.8 11.7 + - - -
46A THR* 3.7 36.9 + - - +
47A GLN* 5.7 0.2 - - - +
246B PRO* 3.9 15.3 - - - +
272B LYS* 3.0 63.8 + - + +
275B LEU* 1.3 80.7 - - + +
277B ASN* 1.3 72.6 + - - +
278B ALA 5.2 0.2 - - - -
279B LYS* 5.3 5.2 + - - -
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Residues in contact with ASN 277 (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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118B GLU* 3.9 23.4 + - - +
119B THR* 3.1 34.2 + - - +
122B ALA* 3.5 13.9 - - + -
244B SER* 5.0 2.2 + - - -
246B PRO* 5.4 1.4 - - - +
273B PHE* 2.8 44.3 + - - +
276B ARG* 1.3 89.8 + - - +
278B ALA* 1.3 67.8 + - - +
279B LYS* 3.6 5.9 - - - +
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Residues in contact with ALA 278 (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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122B ALA* 3.5 25.6 - - - +
123B THR* 3.7 6.1 - - - +
126B ARG* 3.6 31.9 + - - +
274B ILE* 2.9 22.9 + - + +
275B LEU 4.9 3.6 - - - +
276B ARG 5.2 0.3 - - - -
277B ASN* 1.3 80.8 + - - +
279B LYS* 1.3 63.7 + - - +
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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