Contacts of the strand formed by residues 103 - 109 (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 THR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ARG* 5.9 0.9 - - - -
102B LEU* 1.3 73.3 + - - +
104B VAL* 1.3 73.7 + - - +
105B LEU* 3.7 12.2 + - + +
133B VAL* 3.2 7.5 - - - +
134B THR* 2.8 47.0 + - - +
136B PRO* 3.5 24.3 - - - +
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Residues in contact with VAL 104 (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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94B GLU* 3.8 41.3 - - + +
97B VAL* 3.6 28.0 - - + -
98B ARG* 5.4 6.6 - - + +
102B LEU 4.3 0.6 + - - +
103B THR* 1.3 79.8 - - - +
105B LEU* 1.3 63.4 - - - +
106B GLY* 3.7 14.6 - - - +
107B TRP* 4.4 0.4 - - - +
131B ILE* 3.9 28.9 - - + -
132B LEU 3.8 2.9 - - - -
133B VAL* 4.3 1.1 - - + -
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Residues in contact with LEU 105 (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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58B TRP* 3.8 14.7 - - + -
59B PHE* 3.6 33.7 - - + -
62B ARG* 5.8 0.2 - - - -
64B LEU* 4.4 17.4 - - + +
65B PRO 5.2 0.9 - - - +
67B PRO* 4.2 4.0 - - + -
72B LEU* 4.2 7.9 - - + -
103B THR* 4.6 10.1 - - + -
104B VAL* 1.3 75.7 - - - +
106B GLY* 1.3 58.4 + - - +
132B LEU* 2.8 20.5 + - + +
133B VAL* 4.5 1.1 - - - +
134B THR* 3.6 40.4 - - + +
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Residues in contact with GLY 106 (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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58B TRP* 3.8 13.0 - - - -
104B VAL* 3.4 9.5 - - - +
105B LEU* 1.3 81.8 - - - +
107B TRP* 1.3 68.8 + - - -
131B ILE* 3.7 5.0 - - - +
132B LEU* 2.9 27.9 + - - +
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Residues in contact with TRP 107 (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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58B TRP* 3.0 19.2 + - - -
62B ARG* 4.4 5.7 + - - -
77B VAL* 3.9 26.7 - - + -
79B LEU* 4.3 9.2 - - + -
90B ARG* 3.3 47.2 - - + +
93B VAL* 3.9 23.3 - - + -
94B GLU* 2.7 29.3 + - + +
104B VAL* 4.6 0.2 - - + -
106B GLY* 1.3 80.6 - - - -
108B ARG* 1.3 60.0 + - - +
109B GLU 4.2 0.9 + - - -
129B GLU* 3.5 32.3 - - + +
130B GLN 3.2 18.2 - - - -
131B ILE* 3.6 36.2 - - + +
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Residues in contact with ARG 108 (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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54B LEU* 4.4 19.8 + - - +
55B LEU* 3.6 23.7 - - - +
58B TRP* 3.4 37.0 - - + +
62B ARG* 5.7 0.2 - - - +
107B TRP* 1.3 71.2 - - - +
109B GLU* 1.3 69.4 + - - +
110B VAL* 3.4 2.5 + - - +
111B PRO* 3.7 19.9 - - - +
129B GLU* 3.4 4.4 - - - -
130B GLN* 2.8 70.9 + - + +
132B LEU* 4.6 6.0 - - + +
175B TYR* 4.0 1.0 + - - -
190B ASP* 2.8 42.8 + - - -
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Residues in contact with GLU 109 (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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58B TRP* 5.3 0.2 - - - -
86B ARG* 5.2 1.4 + - - -
107B TRP 4.2 1.2 + - - -
108B ARG* 1.3 80.0 - - - +
110B VAL* 1.3 71.0 + - - +
111B PRO* 3.4 9.5 - - - +
127B HIS* 3.6 36.3 + - + +
128B ILE 4.4 1.6 - - - +
129B GLU* 4.2 12.4 + - + +
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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