Contacts of the strand formed by residues 1055 - 1059 (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 ILE1055 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A GLN* 3.5 37.5 - - - +
1030A GLN* 3.9 23.3 - - + +
1031A VAL 3.1 4.1 + - - +
1032A SER* 3.2 24.7 - - - +
1033A VAL 3.0 22.7 + - - -
1053A ALA* 3.6 4.4 - - - +
1054A ASP* 1.3 87.0 - - + +
1056A ILE* 1.3 79.0 - - - +
1057A GLN 4.5 0.7 - - - +
1100A VAL* 4.5 0.2 - - - -
1101A LEU* 3.3 33.2 - - + +
1103A ARG* 4.1 22.0 - - + +
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Residues in contact with ILE1056 (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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1033A VAL 3.5 6.3 - - - +
1035A LEU* 3.7 28.0 - - + -
1045A ALA* 3.6 37.9 - - + +
1048A VAL* 3.8 22.0 - - + -
1049A ALA* 4.5 0.4 - - + +
1055A ILE* 1.3 82.6 - - - +
1057A GLN* 1.3 68.2 + - - +
1058A ILE* 3.9 12.1 + - + +
1087A VAL* 4.9 0.2 - - + -
1091A LEU* 4.4 4.9 - - + -
1100A VAL* 3.7 28.9 - - + +
1101A LEU 2.9 7.1 + - - -
1102A LEU* 3.4 14.7 - - + +
1103A ARG 2.9 24.1 + - - +
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Residues in contact with GLN1057 (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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871A CYS* 6.0 0.5 - - - +
873A GLY* 6.0 3.8 - - - -
964A GLU* 3.6 19.2 + - - +
1032A SER* 5.5 0.9 - - - +
1033A VAL 2.9 8.2 + - - +
1034A LYS* 3.5 31.5 - - + +
1035A LEU* 2.8 32.7 + - - +
1055A ILE* 4.2 2.3 - - + +
1056A ILE* 1.3 74.3 - - - +
1058A ILE* 1.3 68.1 + - - +
1059A SER* 3.4 15.9 + - - +
1103A ARG* 3.4 41.3 + - + +
1105A ASP* 2.8 32.2 + - - -
1126A GLY* 6.0 0.9 - - - -
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Residues in contact with ILE1058 (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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1035A LEU 3.7 2.7 - - - -
1037A ALA* 4.2 10.1 - - + -
1041A ILE* 4.0 14.6 - - + -
1056A ILE* 4.4 6.3 - - + +
1057A GLN* 1.3 75.2 - - - +
1059A SER* 1.3 60.1 + - - +
1080A TRP* 4.6 3.5 - - + +
1083A GLY* 3.8 27.6 - - - +
1084A VAL* 3.8 24.9 - - + +
1087A VAL* 4.0 40.2 - - + -
1102A LEU* 4.2 21.8 - - + -
1103A ARG 2.9 17.5 + - - +
1104A ALA* 3.4 4.9 - - - +
1105A ASP 3.1 24.3 + - - +
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Residues in contact with SER1059 (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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970A GLY 4.2 10.8 - - - -
1034A LYS* 3.4 25.9 - - - +
1035A LEU 2.9 20.0 + - - -
1036A VAL* 3.4 16.5 - - - +
1037A ALA* 2.9 24.9 + - - +
1057A GLN* 3.4 6.6 + - - -
1058A ILE* 1.3 72.4 - - - +
1060A GLY* 1.3 62.0 + - - +
1080A TRP* 4.6 1.8 - - - -
1105A ASP* 3.0 20.8 + - - -
3508A FMN 4.9 1.3 - - - -
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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