Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 3F5O
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 LEU 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B VAL* 4.5 4.0 - - + -
108B LYS* 4.3 0.5 + - - +
109B GLN* 3.7 0.9 - - - -
110B GLY* 2.9 29.0 + - - -
111B LYS 3.8 0.4 - - - -
112B THR* 1.3 91.7 - - - +
114B ALA* 1.3 60.8 + - - +
115B PHE* 4.1 17.3 - - + -
135B THR* 3.9 15.5 - - + -
136B LYS 3.4 13.7 - - - +
137B HIS* 4.1 11.7 - - + +
138B LEU* 4.3 2.7 - - - -
84D VAL* 3.9 24.2 - - + -
113D LEU* 4.4 17.3 - - + -
137D HIS* 4.1 11.2 - - + +
150D COA 3.1 40.4 + - + +
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Residues in contact with ALA 114 (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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72B LEU* 3.7 33.7 - - + -
108B LYS 3.4 9.2 - - - +
109B GLN* 4.2 4.9 - - + -
113B LEU* 1.3 74.5 - - - +
115B PHE* 1.3 63.7 + - - +
116B THR* 5.0 1.1 - - - -
134B HIS 3.8 0.7 - - - +
135B THR* 3.3 5.2 - - - +
136B LYS* 2.9 35.9 + - + +
138B LEU* 4.1 20.2 - - + +
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Residues in contact with PHE 115 (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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106B VAL* 3.7 1.4 - - - +
107B LEU* 2.8 26.9 + - + -
108B LYS* 2.9 29.8 + - + +
113B LEU* 4.1 24.2 - - + -
114B ALA* 1.3 74.9 - - - +
116B THR* 1.3 67.1 + - - +
133B ARG* 5.9 1.1 - - + -
134B HIS 3.7 3.4 - - - -
135B THR* 3.4 15.9 - - + -
89C THR* 3.2 29.4 - - + -
90C TYR 3.9 7.2 - - - -
91C MET* 3.4 34.5 - - + -
84D VAL* 3.5 32.3 - - + -
150D COA 3.5 27.4 - - - -
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Residues in contact with THR 116 (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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68B SER* 3.1 33.9 + - - +
71B ALA* 5.3 0.2 - - + -
72B LEU* 3.9 37.7 - - + -
105B HIS 3.2 13.5 - - - +
106B VAL* 4.2 8.1 - - + -
107B LEU* 4.1 4.9 - - - +
114B ALA 5.0 0.2 - - - -
115B PHE* 1.3 81.7 - - - +
117B SER* 1.3 60.8 + - - +
118B VAL* 5.2 0.2 - - - -
133B ARG* 3.1 10.8 - - - +
134B HIS* 2.9 47.6 + - - +
136B LYS* 5.8 0.2 - - + -
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Residues in contact with SER 117 (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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103B THR 3.8 0.2 - - - +
104B ALA* 3.3 0.3 - - - +
105B HIS* 2.6 71.6 + - - -
107B LEU* 4.0 14.8 - - - +
116B THR* 1.3 75.4 - - - +
118B VAL* 1.3 66.9 + - - +
119B ASP* 5.6 1.3 + - - -
131B GLN* 5.7 4.9 - - - -
132B GLY 3.3 10.3 - - - -
133B ARG* 4.3 0.7 - - - +
131C GLN* 4.2 13.5 - - - -
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Residues in contact with VAL 118 (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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63B LEU 4.9 0.4 - - - +
64B VAL* 3.7 33.2 - - + +
67B ILE* 5.1 0.4 - - + -
68B SER* 3.7 29.6 - - - +
102B ILE* 3.4 32.5 - - + -
103B THR 3.2 9.2 - - - +
104B ALA* 3.8 7.9 - - + -
116B THR* 4.9 0.4 - - - +
117B SER* 1.3 82.4 - - - +
119B ASP* 1.3 67.9 + - - +
120B LEU* 4.1 10.1 - - + +
130B ALA 4.1 0.2 - - - +
131B GLN* 3.2 6.1 - - - +
132B GLY 2.8 35.4 + - - +
134B HIS* 5.7 0.2 - - + -
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Residues in contact with ASP 119 (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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101B VAL 3.5 1.7 - - - +
102B ILE* 3.3 3.5 - - - -
103B THR* 2.8 42.9 + - - +
105B HIS* 6.5 0.4 - - - -
117B SER* 5.6 1.9 + - - -
118B VAL* 1.3 74.2 - - - +
120B LEU* 1.3 61.3 + - - +
121B THR* 4.1 7.4 - - + +
128B LEU* 3.8 21.7 - - + +
130B ALA 3.7 3.8 - - - -
131B GLN* 3.0 32.0 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.5 4.9 - - + -
60B THR* 3.8 28.0 - - + +
63B LEU* 3.9 27.4 - - + -
64B VAL* 3.9 28.3 - - + -
100B ILE* 4.2 12.8 - - + -
101B VAL 3.3 4.5 - - - +
102B ILE* 3.9 13.9 - - + -
118B VAL* 4.1 10.1 - - + +
119B ASP* 1.3 76.0 - - - +
121B THR* 1.3 59.6 + - - +
128B LEU* 3.6 1.0 - - - +
129B ILE* 2.7 39.0 + - + -
130B ALA* 2.9 26.8 + - + +
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Residues in contact with THR 121 (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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100B ILE* 3.3 5.9 - - - +
101B VAL* 2.8 51.2 + - - +
119B ASP* 4.6 8.1 - - + +
120B LEU* 1.3 80.1 - - - +
122B ASN* 1.3 65.6 + - - +
123B LYS* 5.4 0.2 - - - -
126B GLY* 4.1 15.3 - - - +
127B LYS 3.4 6.5 - - - +
128B LEU* 3.7 26.9 - - + +
129B ILE* 3.7 5.4 - - - +
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Residues in contact with ASN 122 (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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92B SER* 5.9 0.7 - - - +
93B PRO 5.6 1.4 + - - -
98B GLU* 3.6 36.6 + - - +
99B ASP 3.8 9.5 + - - +
100B ILE* 6.1 0.2 - - - -
121B THR* 1.3 71.0 - - - +
123B LYS* 1.3 56.9 + - - +
124B ALA* 2.8 24.5 + - - +
125B THR* 3.3 31.0 + - - +
126B GLY* 2.7 34.0 + - - -
127B LYS* 2.9 15.2 + - + +
129B ILE* 3.7 16.1 - - + +
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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