Contacts of the strand formed by residues 103 - 109 (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 THR 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ARG* 5.9 0.4 - - - -
102A LEU* 1.3 73.2 + - - +
104A VAL* 1.3 73.0 + - - +
105A LEU* 3.5 11.9 + - + -
133A VAL* 3.3 8.6 - - - +
134A THR* 2.8 46.0 + - - +
136A PRO* 3.6 23.8 - - - +
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Residues in contact with VAL 104 (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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94A GLU* 3.9 48.2 - - + +
97A VAL* 4.0 22.9 - - + -
98A ARG* 5.4 7.0 - - + +
102A LEU 4.2 0.6 + - - +
103A THR* 1.3 78.4 - - - +
105A LEU* 1.3 63.7 - - - +
106A GLY* 3.6 16.4 - - - +
107A TRP* 4.4 0.4 - - + +
131A ILE* 4.0 24.0 - - + -
132A LEU 3.8 2.7 - - - -
133A VAL* 4.4 0.7 - - - -
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Residues in contact with LEU 105 (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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58A TRP* 3.8 14.5 - - + -
59A PHE* 3.7 32.5 - - + -
64A LEU* 4.3 19.4 - - + +
65A PRO 5.1 1.8 - - - +
67A PRO* 4.4 3.6 - - + -
72A LEU* 4.2 7.0 - - + -
103A THR* 4.6 11.4 - - + +
104A VAL* 1.3 75.0 - - - +
106A GLY* 1.3 58.4 + - - +
132A LEU* 2.8 20.7 + - + +
134A THR* 3.5 40.2 - - + +
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Residues in contact with GLY 106 (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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58A TRP* 3.8 13.2 - - - -
104A VAL* 3.4 8.6 - - - +
105A LEU* 1.3 81.5 - - - +
107A TRP* 1.3 69.8 + - - -
131A ILE* 3.8 5.4 - - - +
132A LEU 2.9 25.1 + - - +
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Residues in contact with TRP 107 (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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58A TRP* 3.0 19.1 + - - -
62A ARG* 4.4 5.0 + - - -
77A VAL* 4.1 17.5 - - + -
79A LEU* 4.0 20.0 - - + -
90A ARG* 3.2 47.6 - - + +
93A VAL* 3.9 26.2 - - + -
94A GLU* 2.7 27.7 + - + +
104A VAL* 4.7 0.9 - - + -
106A GLY* 1.3 79.9 - - - -
108A ARG* 1.3 60.3 + - - +
109A GLU 4.2 1.1 + - - -
129A GLU* 3.5 24.2 - - + +
130A GLN 3.2 18.4 - - - -
131A ILE* 3.7 35.2 - - + +
132A LEU* 4.8 0.4 - - - +
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Residues in contact with ARG 108 (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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54A LEU* 4.1 20.1 + - - +
55A LEU* 3.5 23.8 - - - +
58A TRP* 3.6 36.0 - - + +
107A TRP* 1.3 73.0 - - - +
109A GLU* 1.3 69.3 + - - +
110A VAL* 3.3 3.8 + - - +
111A PRO* 3.7 20.6 - - - +
129A GLU* 3.3 5.5 - - - -
130A GLN* 2.7 70.8 + - + +
132A LEU* 4.6 5.8 - - + +
175A TYR* 4.1 1.2 + - - -
190A ASP* 2.9 43.0 + - - -
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Residues in contact with GLU 109 (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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107A TRP 4.2 1.4 + - - -
108A ARG* 1.3 79.3 - - - +
110A VAL* 1.3 71.9 + - - +
111A PRO* 3.4 8.5 - - - +
127A HIS* 3.7 34.5 + - + +
128A ILE 4.4 1.8 - - - +
129A GLU* 4.3 10.8 + - + +
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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