Contacts of the helix formed by residues 1221 - 1232 (chain B) in PDB entry 4Z4Q
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 GLY1221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1219B ILE 4.2 1.2 + - - -
1220B GLN* 1.3 73.7 - - - +
1222B ARG* 1.3 68.9 + - - +
1223B ASP* 3.0 4.3 + - - -
1224B GLU* 3.1 9.8 + - - +
1225B ILE* 2.9 29.7 + - - +
1236B VAL* 4.1 3.1 - - - -
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Residues in contact with ARG1222 (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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1205B MET* 4.5 14.5 - - + +
1221B GLY* 1.3 72.6 - - - +
1223B ASP* 1.3 63.1 + - - +
1225B ILE* 3.4 13.5 + - - +
1226B LYS* 3.2 21.5 + - + +
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Residues in contact with ASP1223 (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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1221B GLY* 3.1 1.7 - - - -
1222B ARG* 1.3 78.3 - - - +
1224B GLU* 1.3 61.5 + - + +
1226B LYS* 3.0 9.5 + - - +
1227B LYS* 3.0 24.9 + - - +
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Residues in contact with GLU1224 (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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1221B GLY* 3.1 11.5 + - - +
1223B ASP* 1.3 81.1 - - + +
1225B ILE* 1.3 56.0 + - - +
1227B LYS* 3.4 28.0 - - - +
1228B ALA* 2.9 29.8 + - - +
1234B GLY* 3.6 10.3 - - - -
1235B ARG* 2.8 56.7 + - - +
1236B VAL* 4.7 2.2 - - - -
1327B PHE* 5.1 1.5 - - - -
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Residues in contact with ILE1225 (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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1205B MET* 3.9 11.7 - - + -
1209B PRO 4.0 12.3 - - - +
1210B GLY* 4.3 2.0 - - - -
1211B PRO* 4.1 21.5 - - + -
1219B ILE* 4.4 9.9 - - + +
1221B GLY 2.9 21.5 + - - +
1222B ARG* 3.6 11.7 - - - +
1223B ASP 3.2 0.2 - - - -
1224B GLU* 1.3 72.4 - - - +
1226B LYS* 1.3 57.2 + - - +
1228B ALA* 3.3 5.7 + - - +
1229B TYR* 2.7 66.9 + - + +
1236B VAL* 3.9 20.6 - - + -
1327B PHE* 4.6 8.7 - - + -
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Residues in contact with LYS1226 (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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1201B ILE* 4.8 7.5 - - + +
1202B ASP* 5.6 4.5 - - - +
1205B MET* 4.0 22.9 - - + -
1222B ARG* 3.2 11.0 + - + +
1223B ASP* 3.0 11.6 + - - +
1225B ILE* 1.3 72.4 - - - +
1227B LYS* 1.3 71.0 + - - +
1229B TYR* 3.0 3.9 + - - +
1230B GLU* 2.8 30.8 + - - +
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Residues in contact with LYS1227 (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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1223B ASP 3.0 12.8 + - - +
1224B GLU* 3.4 37.7 - - - +
1225B ILE 3.3 0.2 - - - -
1226B LYS* 1.3 78.6 - - - +
1228B ALA* 1.3 51.8 + - - +
1230B GLU* 2.9 8.4 + - - +
1231B THR* 2.7 46.9 + - + +
1233B LYS 3.5 11.9 - - - +
1234B GLY* 4.9 0.7 - - - -
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Residues in contact with ALA1228 (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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1224B GLU 2.9 17.6 + - - +
1225B ILE 3.7 2.7 - - - +
1227B LYS* 1.3 76.1 - - - +
1229B TYR* 1.3 62.0 + - - +
1232B GLY* 2.7 27.9 + - - -
1233B LYS 3.1 18.7 + - - +
1234B GLY* 3.7 0.2 - - - -
1327B PHE* 3.4 48.0 - - + -
1329B MET* 3.9 5.4 - - - +
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Residues in contact with TYR1229 (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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1181B HIS* 2.7 40.1 + + - -
1201B ILE* 3.9 13.8 - - + +
1205B MET* 3.8 18.6 - - + -
1208B LEU* 3.5 29.9 - - + +
1210B GLY* 3.3 17.1 - - - -
1211B PRO* 3.5 1.7 - - + -
1225B ILE* 2.7 43.4 + - + +
1226B LYS* 3.7 6.3 - - - +
1228B ALA* 1.3 73.4 - - - +
1230B GLU* 1.3 58.4 + - - +
1327B PHE* 4.3 17.3 - + - -
1329B MET* 4.7 8.1 - - + -
1341B GLY* 3.7 1.4 - - - -
1342B ILE* 3.1 58.2 + - + +
1343B VAL 4.6 0.2 + - - -
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Residues in contact with GLU1230 (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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1201B ILE* 3.9 32.1 - - + +
1226B LYS* 2.8 21.5 + - - +
1227B LYS* 3.4 6.3 - - - +
1229B TYR* 1.3 79.2 - - - +
1231B THR* 1.3 66.5 + - + +
1232B GLY 3.8 0.2 - - - -
1341B GLY* 4.7 6.5 + - - -
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Residues in contact with THR1231 (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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1227B LYS* 2.7 26.2 + - + +
1230B GLU* 1.3 83.1 - - + +
1232B GLY* 1.3 56.7 + - - +
1233B LYS* 2.9 33.4 + - - +
1339B GLN* 3.6 23.2 + - - +
1340B VAL* 4.5 6.5 + - - +
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Residues in contact with GLY1232 (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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1228B ALA* 2.7 22.9 + - - -
1230B GLU 3.8 0.6 - - - -
1231B THR* 1.3 71.6 - - - +
1233B LYS* 1.3 60.1 + - - +
1327B PHE* 3.3 8.5 - - - +
1328B ASN* 3.4 1.2 - - - -
1329B MET* 2.9 35.9 + - - +
1339B GLN* 4.5 4.5 - - - -
1340B VAL 3.3 25.2 + - - -
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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