Contacts of the strand formed by residues 1127 - 1140 (chain A) in PDB entry 5YS0
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 GLN1127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1098A PHE* 3.5 20.4 - - - -
1116A THR* 3.7 21.6 - - + +
1117A LYS 3.2 15.0 - - - +
1118A LYS* 4.3 10.9 - - + +
1119A LEU* 4.1 4.2 - - - +
1125A PRO* 3.1 21.1 + - - +
1126A LYS* 1.3 80.2 - - + +
1128A THR* 1.3 63.7 + - - +
1155A ASP* 4.5 6.5 + - - +
1102B ASP* 5.0 2.4 - - - +
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Residues in contact with THR1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A THR* 3.4 6.2 - - - +
1117A LYS* 2.8 32.4 + - + +
1119A LEU* 3.5 23.1 - - + -
1127A GLN* 1.3 76.0 - - - +
1129A LYS* 1.3 76.7 + - - +
1130A CYS* 4.4 3.4 - - - -
1153A SER* 3.5 7.0 - - - -
1155A ASP* 3.5 18.8 + - - +
1156A VAL* 3.4 31.3 - - + +
1301A ERG 4.2 12.3 - - + -
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Residues in contact with LYS1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115A TYR 3.6 6.3 - - - +
1116A THR* 4.0 17.9 - - + +
1128A THR* 1.3 90.5 + - - +
1130A CYS* 1.3 66.4 + - - +
1131A ILE* 4.7 7.4 - - + -
1153A SER* 3.3 9.7 - - - -
1154A PRO* 4.3 15.7 - - + -
1155A ASP* 3.0 32.3 + - - +
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Residues in contact with CYS1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A ILE 3.7 1.0 - - - +
1114A THR* 3.3 8.5 - - - -
1115A TYR* 2.7 63.6 + - + +
1117A LYS* 4.1 11.9 - - - -
1128A THR* 3.9 11.0 - - - -
1129A LYS* 1.3 87.5 - - - +
1131A ILE* 1.3 62.9 + - - +
1132A VAL* 3.9 1.7 - - + +
1151A VAL* 4.3 9.0 - - + -
1152A ARG 3.3 7.9 - - - +
1153A SER* 4.3 10.3 - - - -
1301A ERG 4.3 15.5 - - - -
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Residues in contact with ILE1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112A GLU* 4.0 28.0 - - + +
1113A ILE 3.9 1.8 - - - -
1114A THR* 4.1 15.9 - - + -
1129A LYS* 4.7 7.4 - - + -
1130A CYS* 1.3 78.1 - - - +
1132A VAL* 1.3 62.0 + - - +
1133A THR* 4.1 4.3 + - - +
1150A ILE 3.7 1.6 - - - +
1152A ARG* 2.9 48.0 + - + +
1154A PRO* 3.6 37.0 - - + -
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Residues in contact with VAL1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1111A ARG 3.9 0.2 - - - +
1112A GLU* 3.4 9.8 - - - +
1113A ILE* 2.8 51.6 + - + +
1115A TYR* 3.7 28.9 - - + +
1130A CYS* 4.4 3.4 - - + -
1131A ILE* 1.3 76.1 - - - +
1133A THR* 1.3 67.0 + - - +
1134A GLU* 4.5 4.9 - - + +
1149A GLN* 3.9 33.7 - - + +
1150A ILE 3.4 5.6 - - - +
1151A VAL* 3.6 26.2 - - + -
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Residues in contact with THR1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110A ALA* 5.8 2.2 - - + -
1111A ARG 3.9 7.0 - - - +
1112A GLU* 4.9 9.9 + - + +
1131A ILE* 4.6 5.2 + - - +
1132A VAL* 1.3 73.7 + - - +
1134A GLU* 1.3 60.7 + - - +
1135A THR* 4.7 14.5 + - + -
1148A LYS 3.5 1.9 - - - +
1149A GLN* 3.2 4.7 - - - -
1150A ILE* 2.7 61.5 + - + +
1152A ARG* 5.7 2.3 - - - +
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Residues in contact with GLU1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081A TYR* 3.6 16.9 - - - -
1088A ILE* 5.7 3.5 - - - +
1106A PHE* 3.6 12.9 - - + -
1110A ALA* 3.4 1.2 - - - -
1111A ARG* 2.4 84.8 + - + +
1113A ILE* 4.0 11.3 - - + +
1132A VAL* 4.0 5.8 - - + -
1133A THR* 1.3 73.6 - - - +
1135A THR* 1.3 66.3 + - - +
1147A VAL* 3.6 16.3 - - + +
1148A LYS 3.5 2.7 - - - -
1149A GLN* 3.4 31.4 + - + +
1168A PHE* 5.7 0.5 - - - -
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Residues in contact with THR1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106A PHE* 4.4 0.4 - - - -
1109A ASN 3.2 15.3 - - - +
1110A ALA* 3.6 15.9 - - + -
1133A THR* 4.7 11.5 + - + -
1134A GLU* 1.3 82.6 - - - +
1136A ILE* 1.3 62.6 + - - +
1137A GLU* 2.9 26.4 + - - +
1147A VAL* 3.0 7.8 - - - +
1148A LYS* 2.9 44.5 + - - +
1150A ILE* 5.8 0.7 - - - +
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Residues in contact with ILE1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077A PHE* 3.8 34.3 - - + -
1081A TYR* 4.8 0.4 - - + -
1106A PHE* 3.8 43.3 - - + -
1109A ASN* 3.1 40.7 + - - +
1135A THR* 1.3 72.9 - - - +
1137A GLU* 1.3 62.7 + - - +
1138A HIS 4.5 2.7 - - - +
1139A MET* 4.0 31.7 - - + +
1145A PHE* 4.5 6.5 - - + -
1146A MET 3.7 9.9 - - - +
1147A VAL* 4.5 8.5 - - + +
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Residues in contact with GLU1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135A THR* 2.9 28.4 + - - +
1136A ILE* 1.3 73.5 - - - +
1138A HIS* 1.3 82.6 + - + +
1139A MET* 6.6 0.2 - - - -
1146A MET* 2.9 31.1 + - + -
1148A LYS* 3.7 40.7 + - + +
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Residues in contact with HIS1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136A ILE* 3.8 0.9 - - - +
1137A GLU* 1.3 104.6 + - + +
1139A MET* 1.3 63.6 + - - +
1140A ASP 4.0 0.7 - - - -
1144A PHE* 3.8 29.6 - + + -
1145A PHE* 3.0 26.8 - - - +
1146A MET* 3.0 45.8 + - + +
1169A PHE* 5.3 0.4 - - - -
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Residues in contact with MET1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077A PHE* 4.7 16.8 - - + -
1109A ASN* 3.6 32.5 - - - +
1136A ILE* 4.0 20.4 - - + +
1137A GLU 6.6 0.2 - - - -
1138A HIS* 1.3 78.3 - - - +
1140A ASP* 1.3 61.1 + - - +
1141A LEU* 3.7 16.0 + - + +
1144A PHE 4.0 2.5 - - - -
1145A PHE* 4.1 9.6 - - + -
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Residues in contact with ASP1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A LEU* 5.1 1.0 - - - +
1138A HIS 4.0 0.6 - - - -
1139A MET* 1.3 71.1 - - - +
1141A LEU* 1.3 57.4 + - - +
1142A ASN* 2.7 19.4 + - - +
1143A SER* 2.6 51.5 + - - +
1144A PHE* 2.9 38.8 + - + +
1145A PHE* 5.6 0.3 - - - +
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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