Contacts of the strand formed by residues 1025 - 1035 (chain M) 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 GLU1025 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020M GLY* 4.4 2.8 - - - -
1022M VAL* 3.3 42.2 + - + +
1023M LYS 2.9 15.3 - - - +
1024M ASP* 1.3 75.4 - - - +
1026M PRO* 1.3 75.4 - - + +
1027M GLU* 2.6 29.8 + - - +
1028M THR* 3.1 24.5 + - - +
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Residues in contact with PRO1026 (chain M).
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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1020M GLY* 2.8 28.6 + - - -
1024M ASP 4.0 4.5 - - - +
1025M GLU* 1.3 90.9 - - + +
1027M GLU* 1.3 67.2 + - + +
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Residues in contact with GLU1027 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M VAL* 3.7 26.7 - - + +
1018M ALA 3.8 2.7 - - - -
1019M LYS* 4.1 27.3 + - + +
1025M GLU* 2.6 18.8 - - - +
1026M PRO* 1.3 83.6 - - + +
1028M THR* 1.3 60.9 + - - +
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Residues in contact with THR1028 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M VAL* 3.3 7.9 - - - -
1018M ALA 3.0 36.3 + - - -
1021M VAL* 4.2 6.2 - - - +
1022M VAL* 2.6 33.6 - - + +
1025M GLU* 3.1 16.2 + - - +
1027M GLU* 1.3 73.4 - - - +
1029M ARG* 1.3 76.8 + - - +
1030M VAL* 3.5 14.8 + - + +
1066M LEU* 4.1 11.7 - - + -
1080M GLU* 5.8 2.9 - - + -
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Residues in contact with ARG1029 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003M ARG* 5.6 1.0 - - - +
1015M GLU* 2.6 32.5 + - - +
1016M GLY 3.7 5.8 - - - +
1017M VAL* 4.8 7.9 - - + +
1028M THR* 1.3 80.7 - - - +
1030M VAL* 1.3 62.9 + - - +
1080M GLU* 5.2 0.2 - - - +
1081M LEU* 3.1 33.5 + - + +
1083M THR* 3.6 19.1 - - - +
1145M GLU* 3.1 26.9 + - - +
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Residues in contact with VAL1030 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015M GLU* 3.7 2.9 - - - -
1016M GLY 2.9 39.7 + - - +
1018M ALA* 3.8 17.9 - - + +
1028M THR* 3.9 9.9 - - + +
1029M ARG* 1.3 78.6 - - - +
1031M ALA* 1.3 59.2 + - - +
1032M ILE* 3.1 28.5 - - + -
1066M LEU* 3.3 33.7 - - + -
1078M ILE* 3.5 14.8 - - + -
1079M MET 3.3 9.4 - - - +
1081M LEU* 3.7 11.1 - - - +
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Residues in contact with ALA1031 (chain M).
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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12M 741 3.4 53.7 - - + +
1005M LEU* 4.3 7.6 - - + -
1013M VAL* 4.0 8.7 - - + -
1014M TYR 3.4 5.4 - - - +
1030M VAL* 1.3 74.0 - - - +
1032M ILE* 1.3 60.7 + - - +
1077M VAL 3.5 0.5 - - - +
1078M ILE* 3.6 2.4 - - - -
1079M MET 2.8 36.1 + - - +
1081M LEU* 4.0 3.3 - - + +
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Residues in contact with ILE1032 (chain M).
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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12M 741 3.8 1.6 - - - -
999M ILE* 3.6 33.7 - - + -
1001M MET* 4.1 23.3 - - + -
1012M MET 3.7 1.0 - - - +
1013M VAL* 3.4 1.5 - - - -
1014M TYR* 2.6 51.1 + - + +
1015M GLU 4.3 1.1 - - - +
1016M GLY* 4.1 17.5 - - - +
1030M VAL* 3.1 34.8 - - + -
1031M ALA* 1.3 73.9 - - - +
1033M LYS* 1.3 61.6 + - - +
1034M THR* 4.0 0.4 + - - -
1076M LEU* 4.1 20.9 - - + -
1077M VAL 3.4 7.0 - - - +
1078M ILE* 4.2 8.5 - - + -
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Residues in contact with LYS1033 (chain M).
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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12M 741 3.2 54.7 + - + +
1008M GLY* 3.3 5.1 - - - -
1009M SER* 3.0 42.8 + - - +
1010M PHE* 3.2 8.8 - - - +
1011M GLY* 3.9 24.0 - - - +
1012M MET 3.5 3.1 - - - -
1013M VAL* 4.0 9.4 - - + +
1032M ILE* 1.3 72.3 - - - +
1034M THR* 1.3 68.4 + - - +
1035M VAL* 4.4 1.8 - - + -
1047M PHE* 3.7 22.0 - - + -
1075M THR 3.5 1.2 - - - +
1076M LEU* 3.2 8.3 - - - +
1077M VAL* 2.9 33.3 + - + +
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Residues in contact with THR1034 (chain M).
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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1001M MET* 3.5 35.2 - - + -
1011M GLY* 3.7 6.4 - - - -
1012M MET* 3.1 30.2 + - - +
1014M TYR* 4.1 15.5 - - + -
1032M ILE 4.7 0.2 - - - +
1033M LYS* 1.3 75.2 - - - +
1035M VAL* 1.3 62.2 + - - +
1036M ASN* 3.6 5.3 + - - +
1074M PRO* 4.5 11.9 - - + -
1075M THR 3.7 3.8 - - - -
1076M LEU* 3.5 18.2 - - + -
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Residues in contact with VAL1035 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010M PHE* 4.0 22.4 - - + +
1033M LYS* 4.4 5.4 - - + +
1034M THR* 1.3 73.6 - - - +
1036M ASN* 1.3 69.0 + - - +
1039M ALA* 4.3 17.9 - - + -
1043M GLU* 6.1 1.1 - - - +
1044M ARG* 3.4 22.3 + - + +
1047M PHE* 3.2 44.6 - - + -
1074M PRO* 3.7 3.4 - - - +
1075M THR* 3.0 42.7 + - - +
1077M VAL* 4.7 0.2 - - + -
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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