Contacts of the strand formed by residues 1124 - 1130 (chain B) in PDB entry 1G24
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 ILE1124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1046B TYR* 3.7 4.8 - - - -
1047B GLN* 3.5 12.3 - - + +
1049B PHE* 4.8 12.6 - - + -
1058B TRP* 4.2 14.6 - - + -
1120B THR* 3.4 22.2 - - + +
1122B GLU* 3.4 22.7 - - + +
1123B ASN* 1.3 80.7 - - - +
1125B MET* 1.3 63.7 + - - +
1126B LEU* 3.8 19.1 - - + -
1177B LEU* 4.5 3.1 - - + -
1192B PHE 3.4 1.4 - - - +
1194B VAL* 2.8 46.8 + - + +
1200B ALA* 5.3 0.4 - - + -
1215B MET* 3.8 27.6 - - + -
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Residues in contact with MET1125 (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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1046B TYR* 3.5 31.4 - - + +
1047B GLN 2.9 20.6 + - - +
1048B GLU* 4.2 17.9 - - + +
1049B PHE* 5.6 2.3 + - - -
1124B ILE* 1.3 73.6 - - - +
1126B LEU* 1.3 67.6 + - - +
1127B PHE* 3.7 25.4 - - + -
1177B LEU* 3.9 7.3 - - - +
1191B LYS* 3.7 36.1 - - + +
1192B PHE 3.4 10.1 - - - +
1193B LYS* 3.6 29.4 - - + -
1240B THR* 5.1 2.5 - - + -
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Residues in contact with LEU1126 (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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1124B ILE* 3.8 15.9 - - + -
1125B MET* 1.3 83.3 - - - +
1127B PHE* 1.3 62.1 + - - +
1175B THR* 3.4 26.9 - - + +
1176B SER 3.7 4.7 - - - +
1177B LEU* 3.8 28.3 - - + -
1190B THR 3.6 0.9 - - - +
1191B LYS* 3.4 5.4 - - - -
1192B PHE* 2.8 40.3 + - + +
1194B VAL* 3.7 28.9 - - + -
1200B ALA* 4.9 2.2 - - + -
1215B MET* 3.8 15.5 - - + -
1217B LEU* 3.9 22.0 - - + -
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Residues in contact with PHE1127 (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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1048B GLU* 3.6 36.3 - - + -
1049B PHE 5.5 0.2 - - - -
1125B MET* 3.7 20.6 - - + -
1126B LEU* 1.3 76.5 - - - +
1128B ARG* 1.3 62.8 + - - +
1175B THR* 3.1 6.2 - - - -
1176B SER 2.7 44.3 + - - -
1177B LEU 3.5 16.8 - - - -
1178B MET* 3.7 23.8 - - - +
1179B ASN* 4.0 24.7 - - + -
1183B PHE* 3.4 11.8 - - + -
1189B ILE* 4.7 4.3 - - + -
1190B THR 3.4 4.9 - - - +
1191B LYS* 3.7 42.4 - - + -
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Residues in contact with ARG1128 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091B ARG* 6.1 0.8 - - - +
1127B PHE* 1.3 78.8 - - - +
1129B GLY* 1.3 69.9 + - - +
1130B ASP* 2.7 39.0 + - - +
1134B TYR* 5.9 2.1 - - - -
1173B ILE* 4.0 10.0 - - - +
1174B SER* 2.6 52.3 + - - +
1175B THR* 4.2 1.8 - - + -
1183B PHE* 3.4 16.5 - - + -
1189B ILE* 3.5 4.3 - - - +
1190B THR* 2.9 35.4 + - - -
1192B PHE* 3.8 33.4 - - + -
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Residues in contact with GLY1129 (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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1128B ARG* 1.3 88.5 + - - +
1130B ASP* 1.3 69.8 + - - +
1183B PHE* 3.6 20.1 - - - -
1186B ARG* 4.2 11.4 - - - -
1188B ILE 3.1 9.9 - - - -
1189B ILE* 4.0 10.8 - - - -
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Residues in contact with ASP1130 (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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1128B ARG* 2.7 47.1 + - - +
1129B GLY* 1.3 78.5 - - - +
1131B ASP* 1.3 65.6 + - - +
1134B TYR* 3.6 42.2 - - + +
1186B ARG* 3.9 4.2 - - - +
1187B PRO* 3.4 9.5 - - - +
1188B ILE* 2.8 38.5 + - + +
1190B THR* 4.6 6.2 + - - -
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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