Contacts of the strand formed by residues 1030 - 1036 (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 GLN1030 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A LYS 3.6 5.5 + - - -
962A GLN* 3.4 28.4 + - + +
963A LEU 3.0 25.3 + - - +
1028A GLU 3.7 0.6 + - - -
1029A ALA* 1.3 73.0 - - - +
1031A VAL* 1.3 61.8 + - - +
1054A ASP* 3.4 29.5 + - + +
1055A ILE* 3.9 17.0 - - + +
1101A LEU* 5.9 2.8 - - - +
1237A HIS* 5.3 5.5 - - - +
1238A GLU 3.7 8.5 + - - -
1239A PRO* 2.6 33.3 + - - +
1240A VAL* 3.4 9.4 - - + +
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Residues in contact with VAL1031 (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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963A LEU* 3.3 11.0 - - + +
965A ILE* 3.9 22.7 - - + -
1019A ILE* 4.0 19.7 - - + +
1022A LEU* 3.9 29.6 - - + -
1023A HIS* 3.6 28.7 - - + +
1029A ALA 4.1 3.1 - - - +
1030A GLN* 1.3 75.2 - - - +
1032A SER* 1.3 72.8 + - - +
1033A VAL* 5.0 0.2 - - + -
1053A ALA* 3.9 1.6 - - - -
1054A ASP* 2.8 38.8 + - - +
1055A ILE* 3.1 6.1 + - - +
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Residues in contact with SER1032 (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* 5.3 0.5 - - - +
962A GLN* 5.3 1.9 + - - +
963A LEU 2.7 11.9 + - - +
964A GLU* 3.0 35.7 + - - +
965A ILE* 2.8 30.2 + - - +
1030A GLN 4.0 0.8 + - - -
1031A VAL* 1.3 76.9 - - - +
1033A VAL* 1.3 63.4 + - - +
1055A ILE* 3.2 37.0 - - - -
1057A GLN 5.2 1.6 - - - -
1103A ARG* 3.9 6.6 + - - -
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Residues in contact with VAL1033 (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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502A VAL* 4.4 3.1 - - + -
965A ILE* 3.5 9.0 - - + +
967A MET* 3.8 25.6 - - + -
1015A LEU* 4.2 11.4 - - + -
1019A ILE* 4.1 14.6 - - + -
1031A VAL* 5.0 0.4 - - + -
1032A SER* 1.3 78.8 - - - +
1034A LYS* 1.3 61.7 + - - +
1035A LEU* 3.7 16.2 + - + -
1048A VAL* 3.6 37.7 - - + -
1053A ALA* 4.0 10.5 - - + -
1055A ILE 3.0 5.6 + - - +
1056A ILE* 3.5 7.5 - - + +
1057A GLN* 2.9 25.6 + - - +
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Residues in contact with LYS1034 (chain A).
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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874A GLY 4.8 1.6 - - - +
944A GLN* 4.3 3.6 - - - +
964A GLU* 3.7 27.6 + - - +
965A ILE 2.9 13.9 + - - +
966A LYS* 4.1 6.3 - - + -
967A MET* 3.0 29.3 + - - +
968A ALA 3.5 20.1 + - - +
969A GLN* 4.4 5.6 - - - +
1032A SER 4.2 0.4 - - - -
1033A VAL* 1.3 71.1 - - - +
1035A LEU* 1.3 60.8 + - - +
1057A GLN* 3.5 24.7 - - + +
1059A SER* 3.4 25.1 - - - +
3508A FMN 2.8 65.5 + - - +
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Residues in contact with LEU1035 (chain A).
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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501A GLN* 3.4 19.5 - - - +
502A VAL* 3.8 28.3 - - + -
967A MET* 4.2 4.0 - - + -
968A ALA* 4.4 0.9 - - - -
1033A VAL* 3.9 17.9 - - + +
1034A LYS* 1.3 76.8 - - - +
1036A VAL* 1.3 65.1 + - - +
1041A ILE* 3.8 28.5 - - + -
1044A ILE* 4.1 15.5 - - + -
1045A ALA* 4.5 9.4 - - + -
1048A VAL* 4.6 5.2 - - + -
1056A ILE* 3.7 22.7 - - + -
1057A GLN 2.8 10.5 + - - +
1059A SER* 2.9 29.3 + - - -
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Residues in contact with VAL1036 (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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499A PHE* 3.5 26.0 - - + -
501A GLN* 2.9 32.7 + - - -
968A ALA* 3.5 20.4 - - + +
969A GLN 3.3 32.8 - - - +
970A GLY* 3.5 13.7 - - - +
973A PRO* 4.0 10.1 - - + -
1035A LEU* 1.3 74.8 - - - +
1037A ALA* 1.3 74.3 + - - +
1038A GLU 3.3 0.3 + - - -
1041A ILE* 3.5 6.2 - - - +
1059A SER* 3.4 12.3 - - - +
1061A HIS 5.0 1.8 - - - +
1077A GLY* 4.3 6.7 - - - -
1078A SER 4.9 0.9 - - - +
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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