Contacts of the strand formed by residues 113 - 122 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.9 24.5 - - + -
113B LEU* 4.4 23.3 - - + -
137B HIS* 4.2 10.5 - - + +
150B COA 3.2 37.9 + - + +
84D VAL* 4.5 1.6 - - + -
108D LYS 4.3 0.3 - - - +
109D GLN 3.7 0.2 - - - -
110D GLY* 2.7 33.7 + - - +
111D LYS 3.8 0.2 - - - -
112D THR* 1.3 89.9 - - - +
114D ALA* 1.3 58.1 + - - +
115D PHE* 4.2 17.0 - - + -
135D THR* 4.0 15.0 - - + -
136D LYS 3.3 15.9 - - - +
137D HIS* 4.2 9.4 - - + +
138D LEU* 4.2 4.0 - - - -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 3.5 39.7 - - + -
108D LYS 3.4 9.6 - - - +
109D GLN* 4.5 4.5 - - + -
113D LEU* 1.3 75.9 - - - +
115D PHE* 1.3 63.1 + - - +
116D THR* 5.7 0.4 - - - -
134D HIS 4.0 0.9 - - - +
135D THR* 3.4 5.5 - - - +
136D LYS* 2.9 34.0 + - - +
138D LEU* 4.0 17.5 - - + +
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A THR* 3.2 33.4 - - + -
90A TYR 3.6 17.3 - - - -
91A MET* 3.8 24.5 - - + -
84B VAL* 3.7 26.2 - - + -
150B COA 3.6 20.6 - - + -
106D VAL* 3.6 4.4 - - - +
107D LEU* 2.7 30.9 + - + -
108D LYS* 2.8 40.5 + - + +
113D LEU* 4.2 24.5 - - + -
114D ALA* 1.3 74.3 - - - +
116D THR* 1.3 57.8 + - - +
133D ARG* 6.0 1.1 - - + -
134D HIS 3.8 3.6 - - - -
135D THR* 3.5 13.5 - - + -
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Residues in contact with THR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D SER* 3.1 45.2 + - - +
72D LEU* 5.4 7.2 - - + -
105D HIS 2.7 24.5 + - - -
106D VAL* 4.1 6.6 + - - +
107D LEU* 4.2 3.1 - - - +
114D ALA 5.7 0.2 - - - -
115D PHE* 1.3 76.1 - - - +
117D SER* 1.3 61.5 + - - +
133D ARG* 3.2 10.2 - - - +
134D HIS* 2.9 62.8 + - + +
136D LYS* 5.6 2.9 - - + -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN* 4.1 14.2 + - - -
103D THR 3.9 0.6 - - - +
104D ALA* 3.3 0.3 - - - -
105D HIS* 2.9 43.3 + - - +
107D LEU* 3.6 28.8 - - - +
116D THR* 1.3 76.5 + - - +
118D VAL* 1.3 70.2 + - - +
119D ASP* 5.9 0.9 - - - -
131D GLN* 5.8 4.3 - - - -
132D GLY 3.4 9.4 - - - -
133D ARG* 4.4 0.2 - - - -
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU 4.9 0.4 - - - +
64D VAL* 3.6 44.6 - - + +
67D ILE* 5.1 0.4 - - + -
68D SER* 3.7 17.5 - - - +
102D ILE* 3.4 32.5 - - + -
103D THR 3.3 9.4 - - - +
104D ALA* 3.9 8.1 - - + -
116D THR* 5.1 0.7 - - + -
117D SER* 1.3 82.7 - - - +
119D ASP* 1.3 67.8 + - - +
120D LEU* 3.9 12.1 - - + +
131D GLN* 3.3 5.1 - - - +
132D GLY 2.9 32.9 + - - +
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Residues in contact with ASP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL 3.5 1.2 - - - +
102D ILE* 3.5 3.1 - - - -
103D THR* 2.9 42.6 + - - +
117D SER* 5.9 1.2 - - - -
118D VAL* 1.3 73.1 - - - +
120D LEU* 1.3 62.8 + - - +
121D THR* 4.1 8.7 + - + +
128D LEU* 3.9 18.8 - - + +
130D ALA 3.7 2.7 - - - -
131D GLN* 2.9 33.1 - - - +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.4 4.0 - - + -
60D THR* 3.8 28.5 - - + +
63D LEU* 4.0 25.4 - - + -
64D VAL* 4.0 18.4 - - + -
100D ILE* 4.2 13.7 - - + -
101D VAL 3.2 5.4 - - - +
102D ILE* 4.0 14.4 - - + -
118D VAL* 3.9 19.5 - - + +
119D ASP* 1.3 77.4 - - - +
121D THR* 1.3 64.5 + - - +
128D LEU* 3.6 1.4 - - - +
129D ILE* 2.8 38.8 + - + -
130D ALA* 2.9 23.2 + - + +
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE* 3.3 5.5 - - - +
101D VAL* 2.8 50.1 + - - +
103D THR* 5.4 1.4 + - - -
119D ASP* 4.5 10.0 + - + +
120D LEU* 1.3 81.0 - - - +
122D ASN* 1.3 63.5 + - - +
126D GLY* 3.7 23.4 - - - +
127D LYS 3.2 9.2 - - - +
128D LEU* 3.8 18.8 - - + -
129D ILE* 3.7 5.4 - - - +
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Residues in contact with ASN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLU* 2.7 46.5 + - - +
99D ASP 3.8 4.3 - - - +
121D THR* 1.3 72.8 + - - +
123D LYS* 1.3 59.5 + - - +
124D ALA* 2.8 35.0 + - - +
125D THR* 3.1 30.0 + - - +
126D GLY* 2.8 30.3 + - - -
127D LYS* 2.8 14.1 + - + +
129D ILE* 3.7 4.4 - - + +
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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