Contacts of the strand formed by residues 1057 - 1068 (chain B) in PDB entry 5DGY
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 LYS1057 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056B LYS* 1.3 80.0 - - - +
1058B VAL* 1.3 65.3 + - - +
1059B TYR* 3.4 44.1 + - + +
1090B GLN* 4.9 11.2 - - - +
1092B TYR 3.7 4.9 - - - +
1093B PRO* 5.0 2.2 - - + -
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Residues in contact with VAL1058 (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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1023B VAL* 4.5 28.0 - - + -
1046B VAL* 5.1 6.3 - - + -
1048B VAL* 4.1 17.5 - - + -
1053B VAL* 3.6 32.8 - - + -
1057B LYS* 1.3 72.8 - - - +
1059B TYR* 1.3 70.7 + - - +
1090B GLN* 3.9 2.1 - - - +
1091B VAL* 3.0 30.0 + - + -
1092B TYR* 3.0 33.0 + - + +
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Residues in contact with TYR1059 (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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1057B LYS* 3.4 53.9 + - + +
1058B VAL* 1.3 79.4 - - - +
1060B VAL* 1.4 61.7 + - - +
1061B THR* 3.8 20.8 + - + +
1088B ARG* 5.5 10.5 - - + -
1089B VAL* 3.5 8.7 - - - +
1090B GLN* 3.5 38.9 + - + -
1091B VAL* 4.5 1.1 - - - -
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Residues in contact with VAL1060 (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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1025B ILE* 4.8 19.3 - - + -
1046B VAL* 5.0 11.9 - - + -
1059B TYR* 1.4 74.2 - - - +
1061B THR* 1.3 59.1 + - - +
1062B LEU 4.2 0.4 + - - -
1089B VAL* 2.4 61.6 + - + +
1090B GLN 4.1 2.5 - - - +
1091B VAL* 3.5 28.1 - - + +
1119B PHE* 3.6 24.9 - - + -
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Residues in contact with THR1061 (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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1059B TYR* 3.8 21.9 + - + +
1060B VAL* 1.3 85.5 - - - +
1062B LEU* 1.3 64.0 + - - +
1063B THR* 3.8 8.0 + - - -
1086B PHE* 4.5 12.6 - - + -
1087B SER 3.8 2.7 - - - -
1088B ARG* 3.7 24.7 - - + +
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Residues in contact with LEU1062 (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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1042B VAL* 4.7 24.9 - - + -
1060B VAL 4.2 0.8 + - - -
1061B THR* 1.3 75.1 - - - +
1063B THR* 1.4 71.7 + - - +
1064B CYS* 5.1 2.0 - - + +
1085B TYR* 5.0 10.8 - - + -
1086B PHE* 3.5 3.3 - - - -
1087B SER* 2.4 70.4 + - - +
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Residues in contact with THR1063 (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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1061B THR* 3.8 9.4 + - - -
1062B LEU* 1.4 85.1 - - - +
1064B CYS* 1.4 69.3 + - - +
1065B ALA* 3.8 8.6 + - + +
1081B ARG* 5.4 5.6 - - - +
1083B ASP* 3.8 22.9 - - - +
1085B TYR 4.1 1.8 - - - +
1086B PHE* 3.3 25.2 - - + -
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Residues in contact with CYS1064 (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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1062B LEU* 4.2 3.1 - - + +
1063B THR* 1.4 75.4 - - - +
1065B ALA* 1.4 62.8 - - - +
1083B ASP* 3.6 7.8 - - - +
1084B LEU* 3.3 32.1 + - - -
1085B TYR* 2.4 62.1 + - + +
1086B PHE* 4.2 0.4 - - - +
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Residues in contact with ALA1065 (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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1063B THR* 3.8 9.6 + - + +
1064B CYS* 1.4 79.8 - - - +
1066B PHE* 1.3 61.5 + - - +
1067B ARG* 3.8 21.7 + - - +
1081B ARG* 4.2 21.8 - - - +
1083B ASP* 4.0 21.8 - - - +
1084B LEU* 4.4 5.6 - - - +
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Residues in contact with PHE1066 (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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142B PRO* 4.3 24.5 - - + -
1065B ALA* 1.3 71.4 - - - +
1067B ARG* 1.3 77.0 + - - +
1068B TYR* 4.0 19.4 - + + -
1081B ARG* 3.5 16.8 - - - +
1082B ARG* 3.0 30.7 + - + +
1084B LEU* 4.0 34.2 - - + +
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Residues in contact with ARG1067 (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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1063B THR* 6.4 0.2 - - - +
1065B ALA* 3.8 18.2 + - + +
1066B PHE* 1.3 86.6 - - - +
1068B TYR* 1.3 62.6 + - - +
1069B GLY 5.4 1.8 - - - +
1081B ARG* 3.0 51.8 - - - +
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Residues in contact with TYR1068 (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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138B VAL* 4.6 15.0 - - + -
139B VAL* 4.4 27.9 + - + +
142B PRO* 4.4 26.0 - - + +
145B ASN* 3.9 20.2 - - + -
1066B PHE* 4.0 27.8 - + + -
1067B ARG* 1.3 74.3 - - - +
1069B GLY* 1.3 64.2 + - - +
1070B GLN 4.5 0.2 - - - +
1074B ASP* 2.9 29.4 - - + +
1079B THR* 4.9 3.9 + - - +
1080B PHE 3.6 16.0 + - - -
1081B ARG* 3.8 26.3 - - - +
1082B ARG* 3.9 13.1 + - + +
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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