Contacts of the strand formed by residues 1027 - 1035 (chain L) in PDB entry 3F5P
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 GLU1027 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017L VAL* 4.0 33.1 - - + +
1018L ALA 3.8 5.2 - - - -
1019L LYS* 4.7 14.8 + - + +
1025L GLU* 3.4 15.0 - - - +
1026L PRO* 1.3 91.7 - - + +
1028L THR* 1.3 69.9 + - - +
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Residues in contact with THR1028 (chain L).
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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1017L VAL* 3.3 7.7 - - - -
1018L ALA 2.9 36.3 + - - -
1021L VAL* 4.2 9.3 - - - +
1022L VAL* 3.4 21.7 + - + +
1025L GLU* 2.7 28.5 + - - +
1027L GLU* 1.3 75.6 + - - +
1029L ARG* 1.3 77.8 + - - +
1030L VAL* 3.5 9.5 + - + +
1066L LEU* 4.3 9.4 - - + -
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Residues in contact with ARG1029 (chain L).
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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1015L GLU* 2.5 37.6 + - - -
1016L GLY 3.5 8.3 - - - +
1017L VAL* 4.7 8.1 - - + -
1028L THR* 1.3 81.4 - - - +
1030L VAL* 1.3 66.5 + - - +
1080L GLU* 4.9 0.2 - - - -
1081L LEU* 3.4 29.5 + - + +
1083L THR* 3.6 27.1 - - - +
1145L GLU* 4.7 9.9 + - - +
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Residues in contact with VAL1030 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015L GLU* 3.6 2.4 - - - -
1016L GLY 2.9 36.5 + - - +
1018L ALA* 3.8 24.7 - - + +
1028L THR* 3.8 9.4 - - + +
1029L ARG* 1.3 81.6 - - - +
1031L ALA* 1.3 60.0 + - - +
1032L ILE* 3.4 26.5 - - + -
1066L LEU* 3.3 33.2 - - + -
1078L ILE* 3.6 11.0 - - + -
1079L MET 3.3 9.2 - - - +
1081L LEU* 3.7 11.4 - - - +
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Residues in contact with ALA1031 (chain L).
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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13L 741 3.7 51.1 - - + +
1005L LEU* 4.2 2.2 - - + -
1013L VAL* 4.2 3.8 - - + -
1014L TYR 3.3 7.9 - - - +
1030L VAL* 1.3 75.7 - - - +
1032L ILE* 1.3 60.5 + - - +
1078L ILE* 3.7 3.1 - - - -
1079L MET 3.0 34.2 + - - +
1081L LEU* 3.9 12.4 - - + +
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Residues in contact with ILE1032 (chain L).
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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13L 741 3.7 2.0 - - - -
999L ILE* 3.4 27.1 - - + -
1000L THR 4.7 3.6 - - - +
1001L MET* 3.9 30.5 - - + -
1012L MET 3.7 1.2 - - - +
1013L VAL* 3.2 2.0 - - - -
1014L TYR* 2.5 51.0 + - - +
1016L GLY* 4.5 6.1 - - - +
1030L VAL* 3.4 32.3 - - + +
1031L ALA* 1.3 73.2 - - - +
1033L LYS* 1.3 61.0 + - - +
1034L THR* 5.1 0.2 - - - -
1076L LEU* 4.0 23.8 - - + -
1077L VAL 3.6 8.7 - - - +
1078L ILE* 3.9 13.0 - - + -
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Residues in contact with LYS1033 (chain L).
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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13L 741 3.1 44.2 + - + +
1008L GLY* 3.9 2.9 - - - -
1009L SER* 2.6 46.5 + - - +
1010L PHE* 3.2 12.4 - - + +
1011L GLY 4.5 4.3 - - - +
1012L MET 3.2 11.0 - - - +
1013L VAL* 4.1 16.8 - - + +
1032L ILE* 1.3 73.8 - - - +
1034L THR* 1.3 69.5 + - - +
1035L VAL* 4.0 1.3 + - + +
1047L PHE* 3.7 27.8 - - + -
1075L THR 3.4 1.9 - - - +
1076L LEU* 3.4 7.4 - - - -
1077L VAL* 3.2 30.2 + - - +
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Residues in contact with THR1034 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001L MET* 3.6 27.6 - - + -
1011L GLY* 3.5 23.6 - - - -
1012L MET* 2.9 16.5 + - - +
1014L TYR* 4.1 17.2 + - + -
1033L LYS* 1.3 73.3 - - - +
1035L VAL* 1.3 62.7 + - - +
1036L ASN* 3.8 5.5 + - - +
1074L PRO* 4.5 12.3 - - + -
1075L THR 3.6 4.3 - - - -
1076L LEU* 3.5 24.5 - - + -
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Residues in contact with VAL1035 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010L PHE* 4.2 23.3 - - + +
1033L LYS* 4.6 2.9 - - + -
1034L THR* 1.3 74.4 - - - +
1036L ASN* 1.3 59.6 + - - +
1039L ALA* 3.9 24.0 - - + -
1043L GLU* 5.9 0.9 - - + -
1044L ARG* 3.0 38.6 + - + +
1047L PHE* 3.1 48.7 - - + -
1074L PRO* 4.3 1.6 - - - -
1075L THR* 2.9 28.2 + - - +
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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