Contacts of the strand formed by residues 992 - 1001 (chain B) 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 TYR 992 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972B MET* 3.4 30.7 - - + -
973B GLN* 2.8 38.6 + - - +
976B VAL* 3.3 19.5 - - + +
989B PHE* 3.3 24.2 - + - -
991B ARG* 1.3 77.0 + - - +
993B ASN* 1.3 59.9 + - - +
994B ILE* 3.9 15.7 + - + -
1065B SER* 2.6 35.3 + - - -
1066B SER* 3.0 21.7 + - - -
1069B ASN* 4.3 3.8 - - + +
1096B LEU* 5.3 0.4 - - + -
1155B TYR* 3.5 31.6 - + + -
1156B GLN 3.4 8.1 - - - +
1157B ILE* 4.0 8.3 - - + -
1158B MET* 3.6 12.6 - - - +
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Residues in contact with ASN 993 (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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992B TYR* 1.3 71.0 - - - +
994B ILE* 1.3 72.9 + - - +
995B LEU* 3.4 17.1 + - - +
1155B TYR* 3.2 3.5 - - - -
1156B GLN* 2.8 60.2 + - + +
1158B MET* 3.7 24.0 - - + +
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Residues in contact with ILE 994 (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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1052A GLY* 6.0 1.0 - - - -
1053A GLY 5.0 2.8 + - - +
965B PHE* 4.0 16.5 - - + -
969B GLU* 3.5 36.4 + - + +
972B MET* 3.8 36.3 - - + -
973B GLN* 4.0 5.8 - - - +
992B TYR* 3.8 11.8 + - + -
993B ASN* 1.3 78.2 + - - +
995B LEU* 1.3 63.4 + - - +
996B LYS 4.0 4.5 - - - +
997B ILE* 3.7 33.4 - - + -
1153B ILE* 4.1 5.8 - - + -
1154B THR 3.9 4.9 - - - +
1155B TYR* 3.9 9.2 - - + -
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Residues in contact with LEU 995 (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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1053A GLY* 3.6 31.5 + - - +
1054A MET* 3.5 31.6 + - - +
1055A PHE* 5.4 1.8 - - - -
965B PHE* 5.6 2.5 - - - -
993B ASN* 3.8 33.4 - - - +
994B ILE* 1.3 76.5 - - - +
996B LYS* 1.3 63.9 + - - +
1093B HIS* 3.1 45.3 - - + +
1154B THR* 2.8 14.6 + - + +
1155B TYR* 4.1 7.2 - - - -
1156B GLN* 4.0 16.6 - - + +
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Residues in contact with LYS 996 (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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1054A MET* 3.8 32.1 - - - +
1067A LYS* 5.5 6.3 - - - +
1071A TYR* 5.9 0.6 + - - -
1112A ALA 5.0 5.4 - - - +
957B ASP* 2.6 38.7 + - - +
965B PHE* 4.8 3.6 - - - -
994B ILE* 3.7 2.2 - - - +
995B LEU* 1.3 80.7 - - - +
997B ILE* 1.3 71.9 + - - +
998B GLN* 3.3 37.4 - - + +
1152B LEU 3.8 1.2 - - - +
1153B ILE* 4.1 0.3 - - - +
1154B THR* 2.9 44.0 + - - +
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Residues in contact with ILE 997 (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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957B ASP* 3.8 2.3 + - - +
958B LEU* 3.0 39.2 + - + +
965B PHE* 3.7 50.6 - - + +
968B VAL* 3.9 23.3 - - + -
969B GLU* 4.0 7.6 - - + +
994B ILE* 3.7 19.7 - - + -
996B LYS* 1.3 80.5 - - - +
998B GLN* 1.3 65.8 + - - +
1151B TYR* 4.0 29.4 - - + -
1152B LEU 3.6 3.8 - - - +
1153B ILE* 4.2 11.2 - - + -
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Residues in contact with GLN 998 (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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980A ARG* 5.5 6.3 + - - +
1163A SO4 4.5 12.9 + - - -
955B LEU* 4.0 35.1 + - + +
956B ILE 3.3 6.1 - - - +
957B ASP* 4.0 16.0 - - - +
996B LYS* 3.3 38.7 - - + +
997B ILE* 1.3 79.7 - - - +
999B LYS* 1.3 60.2 + - - +
1000B VAL 3.7 0.2 + - - -
1095B GLN* 4.9 1.0 + - - -
1151B TYR* 3.3 5.7 - - - +
1152B LEU* 2.9 62.6 + - + +
1154B THR* 4.5 4.5 + - - -
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Residues in contact with LYS 999 (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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954B ILE 3.7 0.7 - - - +
955B LEU* 3.4 4.5 - - - -
956B ILE* 2.8 48.5 + - + +
958B LEU* 4.5 13.0 - - + +
964B GLU* 2.6 39.5 + - - +
997B ILE 4.2 0.4 + - - -
998B GLN* 1.3 70.9 - - - +
1000B VAL* 1.3 63.8 + - - +
1001B CYS* 3.8 17.7 + - - -
1150B GLU* 3.6 13.2 - - - +
1151B TYR* 4.2 15.5 - - + -
1164B PEG 4.8 20.2 - - - -
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Residues in contact with VAL1000 (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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953B THR* 3.9 20.9 - - + +
954B ILE 3.8 3.1 - - - -
955B LEU* 3.6 18.4 - - + -
999B LYS* 1.3 74.9 - - - +
1001B CYS* 1.3 58.9 + - - +
1002B ASN* 5.1 2.0 - - + +
1005B LEU* 6.2 0.7 - - + -
1040B ILE* 4.1 29.6 - - + +
1148B TYR* 2.7 33.5 + - + +
1149B PRO* 3.2 27.6 - - + +
1150B GLU 2.8 12.3 + - - +
1151B TYR 4.4 0.7 - - - -
1152B LEU* 4.1 22.7 - - + +
1164B PEG 4.2 2.4 - - - +
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Residues in contact with CYS1001 (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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952B GLY 3.5 2.6 - - - +
953B THR* 3.5 1.4 - - - -
954B ILE* 2.9 53.4 + - + +
956B ILE* 3.9 22.0 - - - -
999B LYS* 3.9 27.4 - - - -
1000B VAL* 1.3 77.8 - - - +
1002B ASN* 1.3 61.5 + - - +
1148B TYR* 3.4 2.2 - - - -
1164B PEG 4.0 24.0 - - - +
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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