Contacts of the strand formed by residues 962 - 966 (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 GLN 962 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898B LYS* 3.4 34.1 - - + +
941B ALA 3.0 5.0 + - - +
942B ILE* 3.4 14.7 - - + +
943B LYS 3.0 23.3 + - - -
960B GLY* 4.0 1.2 - - - -
961B LYS* 1.3 83.9 - - + +
963B LEU* 1.3 70.9 + - - +
1029B ALA* 4.2 1.3 - - - -
1030B GLN* 3.3 37.8 + - + +
1032B SER* 5.4 2.1 + - - +
1055B ILE* 3.4 16.4 - - + +
1103B ARG* 3.2 27.5 + - - +
1124B GLU* 5.1 2.8 + - - -
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Residues in contact with LEU 963 (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* 4.7 0.7 - - - -
943B LYS* 3.3 22.9 - - + +
945B ILE* 3.9 9.9 - - + -
957B LEU* 3.6 45.3 - - + +
960B GLY* 4.5 4.3 - - - -
962B GLN* 1.3 83.2 - - - +
964B GLU* 1.3 62.1 + - - +
1022B LEU* 4.1 37.2 - - + +
1025B ILE* 5.1 0.7 - - + -
1026B ASN* 4.4 4.9 - - + -
1029B ALA* 4.1 19.7 - - + -
1030B GLN 2.9 8.6 + - - +
1031B VAL* 3.3 11.2 - - + +
1032B SER* 2.8 26.1 + - - +
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Residues in contact with GLU 964 (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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900B ASN* 3.0 24.3 + - - -
942B ILE* 3.7 14.7 - - + +
943B LYS 2.9 10.7 + - - +
944B GLN* 3.2 24.1 + - + +
945B ILE* 2.7 35.2 + - - +
963B LEU* 1.3 72.6 - - - +
965B ILE* 1.3 70.9 + - - +
966B LYS 3.6 0.9 + - - -
1032B SER* 3.1 26.2 + - - +
1034B LYS* 3.7 26.4 + - + +
1057B GLN* 4.0 14.7 + - - +
1103B ARG* 3.7 14.0 + - - -
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Residues in contact with ILE 965 (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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945B ILE* 3.5 5.8 - - + +
964B GLU* 1.3 71.7 - - - +
966B LYS* 1.3 60.7 + - - +
967B MET* 3.4 26.6 + - + -
1006B HIS* 4.0 7.6 - - + -
1009B ILE* 3.9 5.2 - - + -
1015B LEU* 3.9 9.9 - - + -
1018B LEU* 3.7 34.1 - - + -
1019B ILE* 3.7 30.1 - - + -
1022B LEU* 3.7 28.5 - - + -
1031B VAL* 4.0 6.5 - - + -
1032B SER 2.8 14.2 + - - +
1033B VAL* 3.5 7.7 - - + +
1034B LYS 2.9 26.0 + - - -
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Residues in contact with LYS 966 (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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903B GLU* 2.6 31.9 + - - +
944B GLN* 3.7 21.8 - - + +
945B ILE 3.0 12.9 + - - +
946B ALA* 4.0 14.6 - - + -
947B SER 4.8 0.5 + - - -
964B GLU* 3.6 2.2 + - - -
965B ILE* 1.3 69.1 - - - +
967B MET* 1.3 60.7 + - - +
968B ALA* 4.2 7.4 - - - +
969B GLN* 3.3 35.5 + - - +
972B LYS* 5.3 0.2 - - - +
975B GLU 5.2 4.5 + - - -
976B GLY* 4.9 1.4 - - - -
977B GLY 4.0 12.5 - - - +
1006B HIS* 2.7 22.2 + - - -
1034B LYS* 4.1 14.1 - - + -
3508B FMN 3.3 30.1 - - + +
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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