Contacts of the strand formed by residues 962 - 966 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A LYS* 3.5 33.3 - - + +
941A ALA 3.0 3.8 + - - +
942A ILE* 3.3 15.2 - - + +
943A LYS 2.9 24.2 + - - -
960A GLY* 4.0 1.0 - - - -
961A LYS* 1.3 88.0 - - + +
963A LEU* 1.3 73.4 + - - +
1029A ALA* 4.3 0.9 - - - -
1030A GLN* 3.4 34.1 + - + +
1032A SER* 5.3 1.6 - - - +
1055A ILE* 3.5 16.8 - - + +
1103A ARG* 3.3 27.2 + - - +
1124A GLU* 5.3 2.2 + - - -
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Residues in contact with LEU 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A ILE* 4.7 0.7 - - - -
943A LYS* 3.3 23.3 - - + +
945A ILE* 3.8 10.8 - - + -
957A LEU* 3.6 38.8 - - + +
960A GLY* 4.5 4.3 - - - -
962A GLN* 1.3 85.4 - - - +
964A GLU* 1.3 54.3 + - - +
965A ILE 4.2 0.2 - - - -
1022A LEU* 4.1 36.8 - - + +
1025A ILE* 5.0 0.4 - - + -
1026A ASN* 4.4 11.0 - - + -
1029A ALA* 4.0 19.7 - - + -
1030A GLN 3.0 7.2 + - - +
1031A VAL* 3.3 10.2 - - + +
1032A SER* 2.7 33.2 + - - +
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Residues in contact with GLU 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A GLY 5.0 0.2 + - - -
900A ASN* 2.8 25.0 + - - -
942A ILE* 3.7 15.0 - - + +
943A LYS 2.9 8.9 + - - +
944A GLN* 3.3 22.9 + - + +
945A ILE* 2.7 33.2 + - - -
963A LEU* 1.3 73.4 - - - +
965A ILE* 1.3 68.3 + - - +
1032A SER* 3.0 26.2 + - - +
1034A LYS* 3.7 26.0 + - + +
1057A GLN* 3.6 21.8 + - - +
1103A ARG* 3.6 8.7 + - - -
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Residues in contact with ILE 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A ILE* 3.5 6.3 - - + -
964A GLU* 1.3 71.6 - - - +
966A LYS* 1.3 60.5 + - - +
967A MET* 3.4 28.5 + - + -
1006A HIS* 4.0 7.9 - - + -
1009A ILE* 4.0 4.7 - - + -
1015A LEU* 3.8 10.3 - - + -
1018A LEU* 3.7 36.8 - - + -
1019A ILE* 3.7 30.5 - - + -
1022A LEU* 3.7 19.5 - - + -
1031A VAL* 3.9 11.2 - - + -
1032A SER 2.8 13.0 + - - +
1033A VAL* 3.5 6.3 - - + +
1034A LYS 2.9 26.4 + - - -
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Residues in contact with LYS 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A GLU* 2.7 35.6 + - - +
944A GLN* 3.6 27.6 - - + +
945A ILE 3.0 10.5 + - - +
946A ALA* 3.9 10.7 - - + +
947A SER* 4.8 1.9 + - - -
964A GLU 3.6 1.2 + - - -
965A ILE* 1.3 70.0 - - - +
967A MET* 1.3 61.5 + - - +
968A ALA* 4.1 8.3 - - - +
969A GLN* 3.7 29.7 + - - +
975A GLU 5.1 4.0 + - - -
976A GLY* 4.7 2.2 - - - -
977A GLY 3.9 13.9 - - - +
1006A HIS* 2.8 22.4 + - - -
1034A LYS* 4.1 13.5 - - + -
3508A FMN 3.3 27.1 - - - +
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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