Contacts of the strand formed by residues 1139 - 1149 (chain N) in PDB entry 3O3U
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 ASN1139 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1130N ALA* 5.9 1.3 - - + -
1132N GLU 4.2 3.3 - - - +
1133N LEU* 3.4 27.5 - - + +
1134N THR* 2.9 42.6 + - - +
1137N VAL* 2.7 31.1 + - - +
1138N PRO* 1.3 75.9 + - - +
1140N LYS* 1.3 60.0 + - - +
1141N VAL* 3.2 6.4 + - - +
1193N MET* 3.2 6.4 - - - +
1194N VAL* 2.7 35.9 + - + +
1196N PRO* 3.3 10.9 - - - +
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Residues in contact with LYS1140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128N ASP* 3.8 33.7 + - - +
1129N SER 4.6 0.2 - - - -
1130N ALA* 3.4 25.4 + - + +
1133N LEU* 5.4 0.2 - - - -
1139N ASN* 1.3 71.7 - - - +
1141N VAL* 1.3 64.6 + - - +
1142N GLY* 3.9 8.7 - - - +
1143N THR* 3.5 21.6 + - - -
1191N GLU* 3.5 32.3 + - + +
1192N LEU 4.2 0.7 - - - +
1193N MET* 3.5 24.3 - - + +
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Residues in contact with VAL1141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129N SER* 3.1 24.8 - - - -
1130N ALA 3.4 8.7 + - - +
1133N LEU* 4.8 8.7 - - + -
1139N ASN 3.2 0.8 + - - +
1140N LYS* 1.3 71.8 - - - +
1142N GLY* 1.3 58.3 + - - +
1157N TRP* 4.3 4.7 - - + -
1192N LEU* 2.9 38.1 + - + +
1194N VAL* 3.6 33.9 - - + -
1206N PHE* 3.8 26.5 - - + -
1225N ILE* 3.7 24.8 - - + +
1227N PRO* 4.9 3.1 - - + -
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Residues in contact with GLY1142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126N ILE* 4.1 7.4 - - - -
1127N VAL 3.5 10.8 - - - -
1128N ASP 3.6 11.4 - - - -
1129N SER* 3.9 1.6 - - - -
1140N LYS* 3.3 6.1 - - - +
1141N VAL* 1.3 81.9 - - - +
1143N THR* 1.3 63.1 + - - -
1144N CYS 4.2 0.4 - - - -
1157N TRP* 3.7 8.7 - - - -
1191N GLU* 3.5 2.4 - - - +
1192N LEU 3.0 25.1 + - - +
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Residues in contact with THR1143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125N GLU 3.6 0.2 - - - +
1126N ILE* 3.4 2.5 - - - +
1127N VAL* 2.8 49.8 + - + +
1128N ASP* 4.7 3.4 + - - +
1140N LYS* 3.5 21.8 + - - -
1142N GLY* 1.3 73.9 + - - -
1144N CYS* 1.3 72.8 + - - +
1145N VAL* 4.1 11.2 - - + -
1157N TRP* 4.3 0.4 - - - -
1189N GLN* 4.1 20.0 - - + +
1190N SER 3.4 14.1 - - - +
1191N GLU* 3.7 11.5 + - + +
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Residues in contact with CYS1144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124N PRO* 4.0 20.2 - - - -
1125N GLU 3.3 7.9 - - - -
1126N ILE* 4.4 2.2 - - + +
1143N THR* 1.3 72.7 - - - +
1145N VAL* 1.3 63.2 + - - +
1155N LEU* 3.6 12.7 - - + +
1157N TRP* 3.7 13.2 - - + +
1189N GLN* 3.2 5.5 - - - -
1190N SER 2.8 34.9 + - - +
1208N CYS* 2.0 53.8 - - + -
1222N THR* 4.2 2.0 - - - -
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Residues in contact with VAL1145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123N LYS 4.7 0.7 - - - +
1124N PRO* 3.4 5.6 - - - +
1125N GLU* 2.8 36.3 + - + +
1127N VAL* 4.0 20.9 - - + -
1143N THR* 3.9 17.9 - - + +
1144N CYS* 1.3 81.1 - - - +
1146N SER* 1.3 64.8 + - - +
1147N GLU* 4.0 28.5 - - + +
1187N THR* 4.2 6.7 - - + -
1188N LEU 3.3 9.4 - - - +
1189N GLN* 4.1 17.5 - - + +
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Residues in contact with SER1146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121N PRO* 3.2 29.3 - - - +
1122N GLY 4.3 3.0 + - - -
1123N LYS 5.6 0.2 - - - -
1124N PRO* 4.6 11.2 - - - -
1145N VAL* 1.3 74.1 - - - +
1147N GLU* 1.3 62.5 + - - +
1149N SER* 5.0 1.2 + - - -
1155N LEU* 3.8 25.3 - - - +
1186N PHE 3.9 1.5 - - - +
1187N THR* 3.2 5.2 - - - +
1188N LEU* 2.8 40.1 + - - +
1210N PHE* 3.5 12.1 - - - +
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Residues in contact with GLU1147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121N PRO* 3.3 2.8 - - - +
1122N GLY* 3.0 28.2 + - - -
1123N LYS 5.9 0.2 + - - -
1125N GLU* 5.6 1.9 - - - +
1145N VAL* 4.0 17.0 - - + +
1146N SER* 1.3 79.6 + - - +
1148N GLY* 1.3 59.6 + - - +
1149N SER 3.8 1.3 - - - -
1186N PHE 3.9 2.2 - - - -
1187N THR* 3.5 26.4 - - + +
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Residues in contact with GLY1148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119N GLN* 3.5 23.9 - - - +
1120N ILE 3.8 5.5 - - - +
1121N PRO* 3.8 4.0 - - - -
1147N GLU* 1.3 73.8 - - - +
1149N SER* 1.3 64.5 + - - +
1185N LEU* 3.8 23.9 - - - +
1186N PHE 2.9 10.5 + - - -
1187N THR* 4.5 1.0 + - - -
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Residues in contact with SER1149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119N GLN 3.6 6.3 - - - -
1121N PRO* 3.8 12.3 - - - +
1146N SER* 5.0 0.9 + - - -
1147N GLU 3.8 0.6 - - - -
1148N GLY* 1.3 77.8 - - - +
1150N TYR* 1.3 63.4 + - - +
1151N PRO 3.4 8.2 + - - -
1152N ALA 2.7 24.3 + - - -
1185N LEU* 3.5 3.7 - - - -
1186N PHE* 2.8 44.8 + - - +
1188N LEU* 4.8 2.1 - - - +
1210N PHE* 3.6 23.0 - - - -
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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