Contacts of the strand formed by residues 128 - 137 (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 128 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.9 32.5 - - + +
108A LYS* 5.6 4.3 - - + +
91D MET* 3.3 42.5 - - + +
92D SER* 2.7 25.8 + - - -
119D ASP* 3.9 22.9 - - - +
120D LEU 3.6 14.8 - - - +
121D THR* 3.8 14.6 - - + -
126D GLY 3.6 2.8 + - - -
127D LYS* 1.3 72.0 - - - +
129D ILE* 1.3 57.7 + - - +
130D ALA 3.7 15.5 - - - +
131D GLN* 4.6 5.2 - - + +
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Residues in contact with ILE 129 (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* 4.8 10.1 - - + -
60D THR* 5.3 1.8 - - - +
90D TYR* 3.7 3.6 - - + +
91D MET* 2.8 25.4 + - - -
92D SER* 3.2 33.8 + - - +
93D PRO 4.8 1.6 - - - +
94D ALA* 3.8 17.7 - - + +
98D GLU* 3.5 18.8 - - - +
100D ILE* 3.5 34.5 - - + -
120D LEU* 2.8 19.1 + - + +
121D THR* 3.7 18.4 - - - +
122D ASN* 4.0 7.6 - - + +
127D LYS 4.2 1.1 - - - +
128D LEU* 1.3 74.1 - - - +
130D ALA* 1.3 66.3 + - + +
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Residues in contact with ALA 130 (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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60D THR* 3.8 29.4 - - + -
88D ILE* 4.2 5.6 - - + -
89D THR 3.1 14.8 - - - +
90D TYR* 4.3 5.8 - - + -
91D MET* 4.4 2.2 - - - +
120D LEU* 2.9 34.9 + - + +
128D LEU* 3.6 10.5 - - - +
129D ILE* 1.3 89.1 - - + +
131D GLN* 1.3 63.0 + - - +
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Residues in contact with GLN 131 (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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105A HIS* 5.9 0.2 + - - -
107A LEU* 3.9 22.4 - - - +
117A SER* 3.9 13.2 + - - -
131A GLN* 5.3 7.4 - - - +
133A ARG* 2.8 46.5 - - - +
64D VAL* 5.2 0.9 - - - -
88D ILE* 3.4 5.1 - - - -
89D THR 2.8 31.3 + - - -
91D MET* 4.0 12.2 - - + +
117D SER* 5.8 3.6 - - - -
118D VAL 3.3 6.7 - - - +
119D ASP* 2.9 26.6 - - - +
128D LEU* 4.6 5.1 - - + +
130D ALA* 1.3 76.7 - - - +
132D GLY* 1.3 65.4 + - - +
133D ARG* 5.3 0.4 - - - +
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Residues in contact with GLY 132 (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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133A ARG* 3.4 9.3 + - - -
64D VAL* 4.3 19.2 - - - +
87D ASN 3.0 14.4 - - - -
88D ILE* 4.1 1.8 - - - -
117D SER* 3.4 5.5 - - - -
118D VAL 2.9 32.9 + - - +
131D GLN* 1.3 79.1 - - - +
133D ARG* 1.3 59.2 + - - +
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Residues in contact with ARG 133 (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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87A ASN* 2.8 30.2 + - - -
88A ILE 4.2 0.8 - - - -
89A THR* 2.9 40.5 + - + +
91A MET* 4.2 9.9 - - - -
131A GLN* 2.8 43.8 + - - +
132A GLY* 3.4 9.1 + - - +
133A ARG* 3.3 33.8 - - - +
64D VAL* 4.7 0.6 - - - +
85D ASP 4.0 0.6 - - - +
86D MET* 3.3 5.8 - - - +
87D ASN* 3.0 50.6 + - - +
107D LEU* 4.4 2.2 - - + -
115D PHE* 6.0 0.9 - - + -
116D THR 3.2 22.0 - - - +
117D SER* 4.4 0.7 - - - +
131D GLN* 5.3 0.8 - - - +
132D GLY* 1.3 74.7 - - - +
134D HIS* 1.3 61.5 + - - +
135D THR* 5.9 0.4 - - - +
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Residues in contact with HIS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D VAL* 4.5 5.8 - - + -
65D ASP* 3.2 33.6 + - - -
68D SER* 2.7 23.9 + - - +
83D SER* 2.7 28.0 + - - -
85D ASP 3.5 10.3 - - - -
86D MET* 4.1 19.6 - - + -
114D ALA 4.0 0.7 - - - +
115D PHE* 3.8 1.3 - - - -
116D THR* 2.9 51.8 + - + +
133D ARG* 1.3 79.1 - - - +
135D THR* 1.3 68.9 + - - +
136D LYS* 3.5 25.3 + - + +
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Residues in contact with THR 135 (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* 3.9 2.3 - - - +
84B VAL* 4.1 4.5 - - + -
85B ASP* 2.7 33.4 + - - +
83D SER* 3.9 1.2 - - - -
84D VAL* 2.8 31.4 + - + -
85D ASP 2.9 19.4 + - - +
113D LEU* 4.0 22.2 - - + -
114D ALA 3.4 10.8 - - - +
115D PHE* 3.5 27.9 - - + +
133D ARG* 5.9 0.9 - - - +
134D HIS* 1.3 73.5 + - - +
136D LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 136 (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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65D ASP* 4.7 0.8 + - - -
68D SER* 5.4 0.2 - - - +
69D THR* 2.8 27.1 + - - +
72D LEU* 3.7 24.2 - - + -
80D PRO 2.7 28.0 + - - +
81D GLY* 3.4 3.8 + - - -
82D VAL 3.2 11.4 - - - +
83D SER* 3.5 21.7 + - - +
84D VAL* 4.1 3.6 - - - -
113D LEU* 3.3 8.5 - - - +
114D ALA* 2.9 34.1 + - + +
116D THR* 5.6 0.4 - - + -
134D HIS* 3.5 34.5 - - + +
135D THR* 1.3 78.5 - - - +
137D HIS* 1.3 60.9 + - - +
138D LEU* 4.0 3.1 + - + -
149D UOC 3.0 20.2 + - - -
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Residues in contact with HIS 137 (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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112B THR* 3.6 26.4 + - + -
113B LEU* 4.1 9.6 - - + +
81D GLY* 3.2 2.9 - - - -
82D VAL* 2.8 38.9 + - + +
84D VAL* 3.6 20.3 - - + +
112D THR* 3.4 21.6 + - + -
113D LEU* 4.2 3.6 - - + +
136D LYS* 1.3 72.0 - - - +
138D LEU* 1.3 75.6 + - - +
139D GLY 3.9 1.4 - - - -
150D COA 2.8 69.1 + - + -
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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