Contacts of the strand formed by residues 1101 - 1105 (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 LEU1101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869B ARG* 5.8 1.6 - - - +
1030B GLN* 6.1 1.3 - - - +
1054B ASP 3.0 12.5 + - - +
1055B ILE* 3.4 25.0 - - + -
1056B ILE 2.9 24.9 + - - +
1100B VAL* 1.3 73.4 - - - +
1102B LEU* 1.3 78.9 + - - +
1103B ARG* 3.9 2.9 - - + +
1123B GLU* 3.2 30.1 - - + +
1124B GLU* 3.9 38.6 - - + +
1237B HIS* 3.8 18.7 - - + +
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Residues in contact with LEU1102 (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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1056B ILE* 3.4 15.3 - - + +
1058B ILE* 4.3 11.4 - - + -
1084B VAL* 4.4 3.8 - - + +
1087B VAL* 3.9 33.0 - - + -
1088B HIS* 4.0 16.2 - - + +
1091B LEU* 4.0 0.9 - - + -
1097B ARG* 3.4 37.0 - - - +
1100B VAL* 3.9 19.3 - - + -
1101B LEU* 1.3 81.2 - - - +
1103B ARG* 1.3 60.1 + - - +
1121B GLY 3.9 11.9 - - - +
1122B ALA* 3.7 4.6 - - + -
1123B GLU* 2.9 37.7 + - - -
1124B GLU 3.2 5.0 + - - -
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Residues in contact with ARG1103 (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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871B CYS* 3.5 21.7 - - - +
898B LYS* 3.6 5.3 - - - +
900B ASN* 5.6 0.2 - - - +
942B ILE* 3.7 19.5 - - - +
962B GLN* 3.2 23.6 + - - +
964B GLU* 3.7 19.4 + - - -
1032B SER* 3.9 14.3 + - - -
1055B ILE* 3.9 21.0 - - + +
1056B ILE 2.9 8.0 + - - +
1057B GLN* 3.7 29.9 + - + +
1058B ILE* 2.7 36.2 + - - +
1101B LEU* 3.9 3.7 + - + +
1102B LEU* 1.3 74.5 - - - +
1104B ALA* 1.3 60.0 + - - +
1122B ALA* 4.6 0.4 - - - -
1124B GLU* 2.8 58.6 + - + +
1125B TYR 4.1 1.3 - - - +
1126B GLY* 4.7 3.4 - - - +
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Residues in contact with ALA1104 (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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1057B GLN* 5.2 1.6 - - - -
1058B ILE 3.3 5.6 - - - +
1080B TRP* 4.8 7.9 - - + -
1084B VAL* 3.6 28.7 - - + -
1103B ARG* 1.3 76.7 - - - +
1105B ASP* 1.3 60.5 + - - +
1108B LEU* 3.4 7.8 - - + +
1117B ALA* 4.7 12.1 - - + -
1122B ALA* 3.9 14.1 - - + -
1124B GLU 3.0 8.0 + - - +
1125B TYR* 3.5 1.6 - - + -
1126B GLY 2.8 24.5 + - - -
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Residues in contact with ASP1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B GLY* 5.8 2.4 - - - -
1057B GLN* 2.8 25.3 + - - +
1058B ILE 3.2 8.4 + - - +
1059B SER* 3.0 21.7 + - - -
1060B GLY 2.9 21.8 + - - +
1063B GLY* 5.7 0.9 - - - -
1080B TRP* 3.6 11.1 - - - -
1104B ALA* 1.3 75.0 - - - +
1106B GLY* 1.3 63.8 + - - +
1108B LEU* 4.0 4.7 - - - -
1126B GLY* 3.3 28.9 - - - +
3508B FMN 2.7 36.7 + - - +
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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