Contacts of the strand formed by residues 1030 - 1036 (chain B) in PDB entry 1OFD
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 GLN1030 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961B LYS 3.6 5.5 + - - -
962B GLN* 3.3 29.6 + - + +
963B LEU* 2.9 25.5 + - - -
1028B GLU 3.8 2.0 + - - -
1029B ALA* 1.3 73.2 - - - +
1031B VAL* 1.3 59.9 + - - +
1032B SER 4.1 0.2 - - - -
1054B ASP* 3.5 28.6 + - + +
1055B ILE* 3.8 18.5 - - + +
1101B LEU* 6.1 1.6 - - - +
1237B HIS* 5.4 5.1 - - - +
1238B GLU 3.9 7.5 + - - -
1239B PRO* 2.7 32.2 + - - +
1240B VAL* 3.7 7.4 - - + -
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Residues in contact with VAL1031 (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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963B LEU* 3.3 12.8 - - + +
965B ILE* 4.0 22.7 - - + -
1019B ILE* 4.1 21.3 - - + +
1022B LEU* 3.8 30.7 - - + -
1023B HIS* 3.7 24.0 - - + +
1029B ALA 4.1 2.9 - - - +
1030B GLN* 1.3 75.9 - - - +
1032B SER* 1.3 70.4 + - - +
1033B VAL* 4.9 0.2 - - + -
1053B ALA* 3.9 1.4 - - - -
1054B ASP* 2.8 41.7 + - - +
1055B ILE* 3.1 6.5 + - - +
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Residues in contact with SER1032 (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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942B ILE* 5.0 0.7 - - - +
962B GLN* 5.4 1.9 + - - +
963B LEU 2.8 9.5 + - - +
964B GLU* 3.1 37.5 + - - +
965B ILE* 2.8 31.0 + - - +
1030B GLN 4.1 1.0 + - - -
1031B VAL* 1.3 77.1 - - - +
1033B VAL* 1.3 61.5 + - - +
1055B ILE* 3.1 34.7 - - - +
1057B GLN 5.2 1.8 - - - -
1103B ARG* 3.9 8.7 + - - -
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Residues in contact with VAL1033 (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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502B VAL* 4.5 2.5 - - + -
965B ILE* 3.5 10.1 - - + +
967B MET* 3.8 25.4 - - + -
1015B LEU* 4.3 12.8 - - + -
1019B ILE* 4.1 14.1 - - + -
1031B VAL* 4.9 0.4 - - + -
1032B SER* 1.3 79.7 - - - +
1034B LYS* 1.3 63.2 + - - +
1035B LEU* 3.7 15.6 + - + -
1048B VAL* 3.8 34.1 - - + -
1053B ALA* 4.0 12.8 - - + -
1055B ILE 3.0 6.0 + - - +
1056B ILE* 3.5 6.6 - - + +
1057B GLN 3.0 22.8 + - - +
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Residues in contact with LYS1034 (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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874B GLY 4.9 0.8 - - - +
944B GLN* 4.4 1.8 - - - +
964B GLU* 3.7 27.4 + - - +
965B ILE 2.9 15.6 + - - +
966B LYS* 4.1 8.1 - - + -
967B MET* 3.0 28.4 + - - +
968B ALA 3.5 22.3 + - - +
969B GLN* 4.3 6.1 - - - +
1032B SER 4.2 0.4 - - - -
1033B VAL* 1.3 71.0 - - - +
1035B LEU* 1.3 61.2 + - - +
1057B GLN* 3.6 22.4 - - + +
1059B SER* 3.4 24.9 - - - +
3508B FMN 2.8 65.8 + - - +
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Residues in contact with LEU1035 (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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501B GLN* 3.4 19.3 - - - +
502B VAL* 3.7 29.6 - - + -
967B MET* 4.1 3.4 - - + -
968B ALA 4.5 0.4 - - - -
1033B VAL* 3.9 18.4 - - + +
1034B LYS* 1.3 77.5 - - - +
1036B VAL* 1.3 59.4 + - - +
1041B ILE* 3.8 28.9 - - + -
1044B ILE* 4.1 14.8 - - + -
1045B ALA* 4.5 11.0 - - + -
1048B VAL* 4.5 4.9 - - + -
1056B ILE* 3.8 21.3 - - + -
1057B GLN 2.8 11.4 + - - +
1058B ILE* 4.5 0.7 - - - -
1059B SER* 2.7 34.5 + - - -
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Residues in contact with VAL1036 (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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499B PHE* 3.4 28.3 - - + -
501B GLN* 2.8 33.4 + - - -
968B ALA* 3.5 20.2 - - + +
969B GLN* 3.2 33.9 - - - +
970B GLY* 3.4 13.2 - - - +
973B PRO* 4.0 7.2 - - + -
1035B LEU* 1.3 75.5 - - - +
1037B ALA* 1.3 71.3 + - - +
1038B GLU 3.5 0.3 + - - -
1041B ILE* 3.6 5.2 - - - +
1059B SER* 3.3 13.2 - - - +
1060B GLY 5.0 2.0 - - - -
1077B GLY* 4.2 9.6 - - - -
1078B SER 4.8 0.7 - - - +
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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