Contacts of the strand formed by residues 1147 - 1157 (chain A) in PDB entry YUA9
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 ALA1147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1005A LEU 5.6 0.3 - - - +
1008A ARG* 5.3 2.1 + - - -
1009A TYR* 3.7 8.3 - - - +
1044A PHE* 3.6 20.8 + - + -
1061A PHE* 3.5 31.9 - - + -
1099A CYS* 5.1 0.2 - - + -
1100A ARG 3.1 10.1 - - - +
1101A VAL* 4.2 3.8 - - + -
1141A ILE* 3.7 10.1 - - + +
1144A GLY 3.4 12.6 + - - +
1145A GLU* 3.2 2.9 - - - +
1146A GLN* 1.3 78.3 - - - +
1148A TYR* 1.3 59.8 + - - +
1149A PRO* 4.4 1.0 - - - +
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Residues in contact with TYR1148 (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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1000A VAL* 2.6 32.4 + - + -
1001A CYS* 3.4 1.0 - - - -
1002A ASN* 3.0 26.4 + - + +
1005A LEU* 3.8 26.9 - - + -
1006A TRP* 3.6 41.3 - + + -
1009A TYR* 3.8 20.8 - - + -
1044A PHE* 4.6 0.7 - - - -
1099A CYS* 3.3 3.2 - - - -
1100A ARG* 2.8 37.3 + - + +
1147A ALA* 1.3 75.2 - - - +
1149A PRO* 1.3 79.2 - - + +
1150A GLU* 3.1 28.6 + - + -
1164A PEG 3.6 13.0 - - - -
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Residues in contact with PRO1149 (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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1000A VAL* 3.3 21.4 - - + +
1005A LEU* 5.4 7.9 - - + -
1039A ILE* 4.2 24.0 - - + +
1040A ILE* 4.5 9.6 - - + +
1043A GLY* 5.4 3.1 - - - -
1044A PHE* 4.1 13.8 - - + -
1097A LEU* 4.1 31.6 - - + -
1098A PHE 4.1 0.2 - - - -
1099A CYS* 3.8 11.2 - - - -
1147A ALA 4.4 1.6 - - - +
1148A TYR* 1.3 95.5 - - + +
1150A GLU* 1.3 62.0 + - - +
1151A TYR 3.6 2.2 - - - -
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Residues in contact with GLU1150 (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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999A LYS* 3.6 12.6 - - - +
1000A VAL* 2.8 25.3 + - - +
1006A TRP* 4.1 1.4 - - - -
1028A MET* 4.1 8.7 - - + -
1098A PHE 3.2 8.8 + - - +
1100A ARG* 2.7 53.6 + - + -
1148A TYR* 3.1 22.8 + - + +
1149A PRO* 1.3 74.2 - - - +
1151A TYR* 1.3 87.0 + - + +
1164A PEG 2.9 32.8 + - - -
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Residues in contact with TYR1151 (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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958A LEU* 4.0 13.2 - - + -
964A GLU* 2.5 35.9 + - - +
968A VAL* 4.0 21.6 - - + +
997A ILE* 4.0 24.7 - - + -
998A GLN 3.2 9.9 - - - +
999A LYS* 4.0 16.9 + - + -
1000A VAL* 4.3 3.1 - - - -
1028A MET* 4.1 11.4 - - + -
1096A LEU 3.9 0.2 - - - +
1097A LEU* 3.3 10.4 - - - +
1098A PHE* 3.0 55.7 + + + +
1100A ARG* 5.9 1.3 + - - -
1150A GLU* 1.3 104.1 + - + +
1152A LEU* 1.3 58.6 + - - +
1153A ILE* 4.0 4.2 + - + +
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Residues in contact with LEU1152 (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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955A LEU* 4.3 8.5 - - + -
996A LYS 3.8 1.4 - - - +
997A ILE* 3.5 2.4 - - - -
998A GLN* 2.8 60.1 + - + +
1000A VAL* 4.0 9.9 - - + +
1036A VAL* 3.3 33.9 - - + -
1037A ASN* 4.7 4.0 - - - +
1040A ILE* 4.0 22.7 - - + -
1095A GLN* 3.7 32.3 - - + +
1096A LEU 3.7 7.6 - - - +
1097A LEU* 3.7 11.9 - - + -
1151A TYR* 1.3 70.4 - - - +
1153A ILE* 1.3 61.2 + - - +
1154A THR* 4.0 1.2 + - - +
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Residues in contact with ILE1153 (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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968A VAL* 3.8 23.1 - - + -
972A MET* 3.8 41.7 - - + -
994A ILE* 4.2 16.6 - - + -
996A LYS 3.6 7.2 - - - +
997A ILE* 4.4 10.1 - - + -
1030A PHE* 4.0 8.7 - - + -
1095A GLN* 3.1 7.4 - - - -
1096A LEU* 2.9 38.8 + - + +
1097A LEU 4.9 0.2 - - - -
1098A PHE* 3.8 31.0 - - + +
1151A TYR* 4.5 3.8 - - + +
1152A LEU* 1.3 76.0 - - - +
1154A THR* 1.3 65.3 + - - +
1155A TYR* 3.7 3.8 - - + -
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Residues in contact with THR1154 (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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994A ILE* 3.8 2.9 - - - +
995A LEU* 2.9 31.4 + - + -
996A LYS* 2.8 33.3 + - + +
998A GLN* 4.6 7.1 + - - -
1093A HIS* 4.0 29.6 - - + +
1094A ARG 3.3 9.6 - - - +
1095A GLN* 3.1 28.0 + - + +
1152A LEU* 4.8 1.4 + - - +
1153A ILE* 1.3 71.2 - - - +
1155A TYR* 1.3 67.2 + - - +
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Residues in contact with TYR1155 (chain A).
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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972A MET* 3.8 10.1 - - + -
992A TYR* 3.4 33.0 - + - -
993A ASN 3.3 12.8 - - - +
994A ILE* 4.1 16.8 - - + -
995A LEU* 4.2 5.4 - - - -
1069A ASN* 2.7 29.1 + - - -
1072A VAL* 3.6 11.3 - - - +
1093A HIS* 3.6 4.5 - - - -
1094A ARG* 2.8 65.9 + - + +
1096A LEU* 3.5 40.5 - - + +
1153A ILE* 3.7 10.1 - - + -
1154A THR* 1.3 77.8 - - - +
1156A GLN* 1.3 68.5 + - - +
1157A ILE* 4.2 2.2 - - + -
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Residues in contact with GLN1156 (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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992A TYR* 3.3 7.4 - - - +
993A ASN* 2.8 60.7 + - + +
995A LEU* 4.1 7.1 - - + +
1090A TYR 3.9 13.3 + - - +
1091A ILE* 2.7 32.8 + - - +
1092A CYS 3.9 9.0 - - - +
1093A HIS* 3.8 23.6 + - + -
1094A ARG* 5.4 0.7 - - - +
1155A TYR* 1.3 83.5 - - - +
1157A ILE* 1.3 66.1 + - - +
1158A MET* 5.5 0.9 - - + -
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Residues in contact with ILE1157 (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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986A GLY 3.8 11.4 - - - +
987A GLY* 4.0 13.2 - - - -
989A PHE* 3.8 32.3 - - + -
991A ARG 4.1 4.3 - - - -
992A TYR* 4.0 14.6 - - + -
1069A ASN* 4.0 7.6 - - - +
1088A SER 4.0 3.6 - - - +
1089A CYS 3.5 17.2 + - - +
1090A TYR* 3.5 36.1 - - + +
1094A ARG* 3.5 37.6 - - - +
1155A TYR* 4.2 3.5 - - + -
1156A GLN* 1.3 82.8 - - - +
1158A MET* 1.3 59.9 + - - +
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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