Contacts of the helix formed by residues 1208 - 1219 (chain B) in PDB entry 1AIS
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 PRO1208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1205B PHE* 6.1 1.6 - - + -
1206B VAL 4.4 2.0 - - - +
1207B LYS* 1.3 88.6 - - + +
1209B THR* 1.3 61.7 + - + +
1211B TYR* 3.1 30.0 + - + +
1212B VAL 3.7 2.4 + - - -
1233B LEU* 4.2 26.2 - - + -
1242B THR* 5.9 3.6 - - + -
1247B PRO* 4.4 31.6 - - + +
1250B LEU* 4.7 13.9 - - + -
1251B VAL* 3.8 9.0 - - + +
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Residues in contact with THR1209 (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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1207B LYS* 3.4 27.4 - - + +
1208B PRO* 1.3 77.9 - - + +
1210B ASP* 1.3 62.3 + - - +
1211B TYR 3.1 1.9 + - - -
1212B VAL* 3.3 23.5 + - - +
1213B ASN* 4.6 3.1 + - - +
1230B ILE* 3.8 38.3 - - + +
1233B LEU* 3.8 25.6 - - + -
1234B ASP* 4.0 13.8 + - - +
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Residues in contact with ASP1210 (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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1167B LYS* 3.9 30.8 - - - +
1169B PRO* 3.2 22.3 - - + +
1205B PHE 4.6 0.2 - - - +
1206B VAL* 3.5 24.2 - - + +
1207B LYS* 2.8 52.5 + - - +
1209B THR* 1.3 78.9 + - - +
1211B TYR* 1.3 57.6 + - + +
1213B ASN* 4.8 6.0 + - - +
1214B LYS 5.1 0.5 + - - -
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Residues in contact with TYR1211 (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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132A GLU* 3.9 20.4 + - - -
1160B TYR* 6.0 0.3 - - - -
1169B PRO* 3.2 33.7 - - + -
1170B ARG 4.2 5.4 + - - -
1171B THR* 3.9 23.3 + - + +
1206B VAL* 4.5 19.1 - - + +
1207B LYS 3.6 17.9 - - - -
1208B PRO* 3.1 14.8 + - + +
1210B ASP* 1.3 78.9 - - - +
1212B VAL* 1.3 63.8 + - - +
1213B ASN 3.3 3.3 + - - -
1214B LYS* 3.4 12.5 + - - +
1215B PHE* 3.1 48.5 + + + +
1247B PRO* 3.8 28.4 - - + +
1248B ALA 5.6 1.8 - - - -
1251B VAL* 4.2 9.4 - - + -
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Residues in contact with VAL1212 (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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1209B THR* 3.3 18.0 + - - +
1211B TYR* 1.3 77.1 - - - +
1213B ASN* 1.3 60.0 + - - +
1215B PHE* 3.8 0.5 - - - +
1216B ALA* 2.8 33.4 + - - +
1226B ARG* 3.8 39.7 - - + +
1229B ALA* 4.3 7.4 - - + -
1230B ILE* 4.1 14.1 - - + -
1233B LEU* 3.5 31.4 - - + -
1251B VAL* 3.7 14.1 - - + -
1255B LEU* 4.3 12.3 - - + +
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Residues in contact with ASN1213 (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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1209B THR 4.6 3.4 + - - +
1210B ASP 4.8 5.1 + - - +
1211B TYR 3.3 0.6 - - - -
1212B VAL* 1.3 76.7 - - - +
1214B LYS* 1.3 66.6 + - - +
1216B ALA 3.3 0.2 + - - -
1217B ASP* 2.9 32.9 + - - +
1223B GLU* 4.3 6.3 + - - -
1226B ARG* 3.2 36.3 + - - +
1230B ILE* 5.5 6.3 - - - +
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Residues in contact with LYS1214 (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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1169B PRO* 3.2 52.3 + - + +
1170B ARG* 3.2 32.1 - - - +
1171B THR* 5.1 1.2 - - - +
1174B GLU* 4.1 14.1 + - - -
1211B TYR* 3.4 7.7 + - - +
1213B ASN* 1.3 76.4 - - - +
1215B PHE* 1.3 96.7 + - - +
1217B ASP* 3.1 19.7 + - - +
1218B GLU* 3.2 27.5 + - + +
1276B ARG* 4.6 3.8 - - - +
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Residues in contact with PHE1215 (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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1171B THR* 4.6 10.1 - - + -
1211B TYR* 3.1 30.2 + + + +
1214B LYS* 1.3 112.4 - - - +
1216B ALA* 1.3 57.0 + - - +
1218B GLU* 3.4 18.1 + - - +
1219B LEU* 3.0 34.6 + - - +
1248B ALA* 4.9 3.1 - - - -
1251B VAL* 3.7 33.7 - - + -
1255B LEU* 3.5 18.8 - - + -
1274B VAL* 3.5 29.8 - - + +
1275B ALA* 3.9 27.8 - - + -
1276B ARG* 4.3 4.7 - - - -
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Residues in contact with ALA1216 (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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1212B VAL 2.8 21.1 + - - +
1213B ASN 3.7 0.2 - - - +
1215B PHE* 1.3 74.0 - - - +
1217B ASP* 1.3 58.8 + - - +
1219B LEU* 3.4 8.2 + - - +
1220B GLY 3.1 6.2 + - - -
1221B LEU* 2.7 34.5 + - - +
1225B VAL* 5.8 1.6 - - + -
1226B ARG* 3.4 38.6 - - + +
1255B LEU* 4.3 12.8 - - + +
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Residues in contact with ASP1217 (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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1213B ASN* 2.9 21.6 + - - +
1214B LYS* 3.3 11.8 - - + +
1216B ALA* 1.3 77.4 - - - +
1218B GLU* 1.3 62.2 + - + +
1220B GLY* 3.4 11.4 + - - -
1221B LEU* 4.2 9.0 + - - +
1226B ARG* 2.6 26.4 + - - +
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Residues in contact with GLU1218 (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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1214B LYS* 3.2 27.4 + - + +
1215B PHE* 3.7 27.4 - - - +
1217B ASP* 1.3 78.7 - - + +
1219B LEU* 1.3 63.1 + - - +
1274B VAL* 4.0 32.2 - - + +
1276B ARG* 4.2 11.4 + - - -
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Residues in contact with LEU1219 (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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1215B PHE 3.0 26.4 + - - +
1216B ALA* 3.4 7.2 + - - +
1217B ASP 3.3 0.2 - - - -
1218B GLU* 1.3 77.6 - - - +
1220B GLY* 1.3 53.2 + - - +
1255B LEU* 4.2 18.2 - - + -
1266B ARG* 2.5 63.6 + - + +
1270B GLU* 3.8 17.5 - - + +
1271B VAL* 4.5 12.3 - - + -
1274B VAL* 3.5 38.6 - - + -
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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