Contacts of the strand formed by residues 1140 - 1149 (chain A) in PDB entry 1UX6
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 VAL1140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968A LEU 3.5 2.3 - - - +
969A VAL* 3.2 4.2 - - - -
970A GLN* 3.0 27.7 + - + +
994A PHE* 4.7 4.3 - - + -
995A PHE 3.7 3.6 - - - +
996A ILE* 3.9 10.1 - - + -
1005A ALA* 4.1 16.8 - - + -
1134A VAL* 4.0 14.8 - - + -
1137A GLN* 3.3 44.2 - - + +
1139A MET* 1.3 74.1 - - - +
1141A PHE* 1.3 61.6 + - - +
1142A PHE* 3.4 38.6 + - + -
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Residues in contact with PHE1141 (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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967A GLU* 3.4 29.6 - - + +
968A LEU 3.6 4.0 - - - -
969A VAL* 3.3 38.4 - - + -
993A THR* 3.7 0.5 - - - +
994A PHE* 3.1 4.2 - - - -
995A PHE* 2.8 54.1 + + + +
997A ASN* 3.5 38.1 - - + -
1139A MET* 3.5 23.3 - - + -
1140A VAL* 1.3 74.5 - - - +
1142A PHE* 1.3 61.7 + - - +
1143A SER* 5.0 1.0 + - - -
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Residues in contact with PHE1142 (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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959A TRP* 3.9 27.6 - + - -
967A GLU* 3.5 2.4 - - - -
968A LEU* 2.7 44.1 + - + +
993A THR 3.3 4.0 - - - +
994A PHE* 4.0 18.6 - - + -
1006A GLY* 3.3 22.4 - - - -
1092A TRP* 3.9 13.7 - + - -
1132A LEU* 3.6 38.6 - - + -
1133A PHE 3.6 22.2 - - - -
1134A VAL* 3.9 6.5 - - + -
1140A VAL* 3.4 30.1 - - + -
1141A PHE* 1.3 73.5 - - - +
1143A SER* 1.3 65.3 + - - +
1145A LEU* 4.9 4.3 - - + -
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Residues in contact with SER1143 (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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967A GLU* 3.8 31.5 + - - +
993A THR* 2.9 43.8 + - - +
1141A PHE 5.0 1.0 + - - -
1142A PHE* 1.3 77.7 - - - +
1144A ASP* 1.3 73.2 + - - +
1145A LEU* 3.4 10.6 + - - +
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Residues in contact with ASP1144 (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 GLY* 3.7 0.5 - - - -
993A THR* 4.4 4.0 + - - +
1091A ARG* 2.6 57.6 + - - +
1143A SER* 1.3 81.2 - - - +
1145A LEU* 1.3 61.0 + - - +
1146A LYS* 4.5 13.0 + - - +
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Residues in contact with LEU1145 (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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937A THR* 4.0 14.6 + - - +
939A PHE* 3.6 51.4 - - + -
942A PHE* 4.0 12.1 - - + -
990A PHE* 4.7 1.6 - - + -
991A SER 3.6 3.6 - - - +
992A GLY* 3.8 15.3 - - - -
1092A TRP* 3.9 21.1 - - + -
1132A LEU* 4.0 22.2 - - + -
1142A PHE* 4.9 1.6 - - + -
1143A SER* 3.7 23.8 - - - +
1144A ASP* 1.3 75.9 - - - +
1146A LYS* 1.3 64.4 + - - +
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Residues in contact with LYS1146 (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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937A THR* 4.4 7.0 - - - +
990A PHE* 3.3 4.4 - - - -
991A SER* 2.9 43.6 + - - +
1091A ARG* 3.0 26.8 - - - +
1093A ARG* 6.1 0.8 - - - +
1144A ASP* 4.1 14.5 + - - +
1145A LEU* 1.3 81.0 - - - +
1147A TYR* 1.3 68.0 + - - +
1148A GLU* 6.3 1.1 - - + -
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Residues in contact with TYR1147 (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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927A ILE* 3.6 36.9 - - + +
928A CYS* 5.3 0.2 - - - -
934A ILE* 4.4 1.3 - - + -
937A THR* 3.8 16.7 + - + -
938A ASP* 2.8 22.3 + - - -
939A PHE* 3.4 43.5 - + - -
983A ASP* 2.4 29.3 + - + +
985A PHE* 3.4 32.5 - + - -
988A VAL* 4.3 2.7 - - + -
989A ASP 3.2 12.1 - - - +
990A PHE* 4.3 0.2 - - + -
1130A LEU* 3.7 21.5 - - + -
1146A LYS* 1.3 78.7 - - - +
1148A GLU* 1.3 72.3 + - - +
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Residues in contact with GLU1148 (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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927A ILE* 3.5 29.5 - - + +
928A CYS* 4.4 1.6 - - - -
985A PHE* 5.3 0.4 - - - -
988A VAL* 3.4 5.5 - - - +
989A ASP* 2.9 35.8 + - + +
1146A LYS* 6.3 0.7 - - + -
1147A TYR* 1.3 82.0 - - - +
1149A CYS* 1.3 65.6 + - - +
1150A ARG* 3.3 33.5 + - - +
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Residues in contact with CYS1149 (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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863A ASN* 5.8 0.7 - - - -
927A ILE 3.1 9.9 + - - +
928A CYS* 2.0 52.2 - - + -
929A PRO* 5.0 6.5 - - + +
931A ASN* 4.6 8.7 - - + -
934A ILE* 4.4 5.6 - - - -
984A GLU 5.6 0.4 - - - -
985A PHE* 3.9 19.7 - - - -
986A ASN 6.2 0.2 - - - -
987A ALA 3.6 7.0 - - - +
988A VAL* 4.5 0.9 - - - +
1148A GLU* 1.3 74.8 - - - +
1150A ARG* 1.3 77.6 + - - +
1151A ASP* 3.6 19.7 - - + +
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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