Contacts of the strand formed by residues 1094 - 1102 (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 ARG1094 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986B GLY* 3.1 22.9 + - - -
1069B ASN* 3.1 30.6 + - - +
1072B VAL* 4.5 10.3 - - + +
1073B TYR* 3.6 40.5 + - + +
1087B ARG 3.0 23.2 + - - -
1089B CYS* 3.2 33.7 + - - +
1092B CYS 4.1 6.6 + - - +
1093B HIS* 1.3 72.6 - - - +
1095B GLN* 1.3 66.5 + - - +
1154B THR* 3.1 6.1 - - - +
1155B TYR* 2.8 60.7 + - + +
1157B ILE* 3.6 19.4 - - - +
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Residues in contact with GLN1095 (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* 5.4 3.6 - - - +
1112A ALA* 3.1 33.3 + - + +
1131A VAL* 5.1 0.7 - - - +
998B GLN* 4.9 1.4 + - - -
1032B GLY* 5.3 0.2 - - - -
1033B SER 5.0 0.9 - - - +
1036B VAL* 4.1 20.5 - - + +
1037B ASN* 3.3 24.9 + - - +
1072B VAL* 3.7 21.9 - - - +
1093B HIS 5.4 1.1 - - - +
1094B ARG* 1.3 82.3 - - - +
1096B LEU* 1.3 58.9 + - - +
1152B LEU* 3.9 35.4 - - + +
1153B ILE 3.1 7.0 - - - +
1154B THR* 3.1 23.9 + - - +
1155B TYR* 3.8 3.8 - - - -
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Residues in contact with LEU1096 (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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972B MET* 3.8 28.5 - - + -
992B TYR* 5.0 0.4 - - - +
1030B PHE* 4.4 12.3 - - + -
1031B HIS 3.7 3.4 - - - +
1032B GLY* 3.6 27.8 - - - -
1036B VAL* 4.8 2.0 - - - -
1065B SER* 3.8 19.5 - - - +
1068B SER* 3.6 24.5 - - - +
1069B ASN* 3.9 1.6 - - + +
1072B VAL* 3.7 10.3 - - + -
1095B GLN* 1.3 71.6 - - - +
1097B LEU* 1.3 67.6 + - - +
1152B LEU* 3.7 5.5 - - - +
1153B ILE* 2.8 37.5 + - + +
1155B TYR* 3.5 21.7 - - + +
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Residues in contact with LEU1097 (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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1000B VAL* 4.9 0.4 - - + -
1029B LEU 3.8 0.3 - - - +
1030B PHE* 3.2 7.3 - - - +
1031B HIS* 2.8 39.2 + - + +
1036B VAL* 3.9 22.0 - - + -
1039B ILE* 3.5 36.6 - - + -
1040B ILE* 3.4 26.5 - - + -
1044B PHE* 4.3 8.3 - - + -
1096B LEU* 1.3 75.8 - - - +
1098B PHE* 1.3 60.4 + - - +
1099B CYS* 3.7 13.9 - - - -
1149B PRO* 3.9 13.7 - - + -
1151B TYR 3.2 13.9 - - - +
1152B LEU* 3.8 16.2 - - + -
1153B ILE* 5.0 0.4 - - - -
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Residues in contact with PHE1098 (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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967B SER 5.6 0.4 - - - -
968B VAL* 4.1 22.2 - - + -
971B GLU* 3.5 30.5 - - + -
1028B MET* 3.6 53.8 - - + -
1029B LEU 3.6 9.9 - - - -
1030B PHE* 3.4 33.7 - + + -
1096B LEU 4.3 0.4 + - - -
1097B LEU* 1.3 71.9 - - - +
1099B CYS* 1.3 59.7 + - - +
1150B GLU* 3.2 8.7 + - - +
1151B TYR* 2.9 48.5 + + + -
1153B ILE* 3.9 17.9 - - + +
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Residues in contact with CYS1099 (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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1027B ARG 3.5 0.3 - - - +
1028B MET* 3.1 11.5 - - - -
1029B LEU 2.7 36.9 + - - +
1031B HIS* 4.2 1.8 - - - -
1044B PHE* 3.7 18.4 - - + -
1061B PHE* 3.6 31.6 - - + -
1097B LEU* 3.7 22.4 - - - -
1098B PHE* 1.3 74.0 - - - +
1100B ARG* 1.3 61.0 + - - +
1101B VAL* 3.7 6.4 + - + +
1148B TYR 3.4 10.3 - - - +
1149B PRO* 3.7 16.2 - - + -
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Residues in contact with ARG1100 (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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1006B TRP* 4.0 13.7 - - - -
1009B TYR* 3.5 19.0 - - + +
1013B ARG* 4.4 2.5 - - - +
1026B GLU* 2.9 51.0 + - + +
1027B ARG 3.4 3.8 - - - -
1028B MET* 3.7 24.8 - - - +
1099B CYS* 1.3 69.9 - - - +
1101B VAL* 1.3 58.6 + - - +
1147B ALA* 3.2 2.8 - - - -
1148B TYR* 2.9 36.0 + - + +
1150B GLU* 2.7 44.0 + - - +
1151B TYR* 6.0 0.4 - - - -
1164B PEG 5.2 1.8 + - - -
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Residues in contact with VAL1101 (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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1009B TYR* 3.7 4.2 + - - -
1026B GLU* 3.2 1.7 - - - -
1027B ARG* 2.8 40.4 + - - +
1029B LEU* 4.2 14.4 - - + -
1061B PHE* 3.8 43.5 - - + -
1099B CYS* 3.8 12.3 - - + +
1100B ARG* 1.3 78.6 - - - +
1102B THR* 1.3 63.3 + - - +
1103B LEU* 3.5 23.6 + - + +
1141B ILE* 4.1 17.3 - - + -
1146B GLN 3.5 8.7 - - - +
1147B ALA* 3.9 4.7 - - + -
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Residues in contact with THR1102 (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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1009B TYR* 2.8 26.8 + - - -
1013B ARG* 3.5 20.0 - - - +
1016B VAL* 3.7 35.0 - - + -
1024B ALA* 3.3 27.0 - - + +
1025B ASN 4.1 1.1 - - - -
1026B GLU* 4.3 2.4 + - - +
1101B VAL* 1.3 74.9 - - - +
1103B LEU* 1.3 58.0 + - - +
1141B ILE* 4.2 1.9 - - - +
1146B GLN* 2.8 44.5 + - + +
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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