Contacts of the helix formed by residues 108 - 119 (chain B) in PDB entry 3E5X
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 SER 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B THR 4.3 6.1 - - - -
52B SER* 4.1 11.2 + - - -
87B LEU* 3.9 1.8 - - - -
106B TRP 4.0 3.0 + - - -
107B PHE* 1.3 76.5 - - - +
109B GLU* 1.4 66.2 - - - +
110B LYS* 3.5 9.5 + - - +
111B SER* 3.0 26.6 + - - -
112B LEU* 3.0 22.0 + - - +
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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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9A ASP* 4.7 2.8 - - - +
124A PHE* 3.6 25.8 - - + +
128A LYS* 4.6 5.0 + - - -
51B THR 4.6 1.6 + - - -
87B LEU* 3.6 18.7 - - + +
88B TYR* 2.5 35.8 + - + +
108B SER* 1.4 73.2 - - - +
110B LYS* 1.3 57.9 + - - +
112B LEU* 3.3 7.6 + - - +
113B ARG* 2.9 61.0 + - - +
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Residues in contact with LYS 110 (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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108B SER* 3.3 8.3 + - - +
109B GLU* 1.3 79.0 + - - +
111B SER* 1.3 62.4 + - - +
113B ARG* 3.4 23.6 + - - +
114B THR* 3.4 18.8 + - - +
170C ASP* 5.4 10.6 + - - -
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Residues in contact with SER 111 (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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31B MET* 3.1 28.2 - - - +
32B GLY* 4.6 1.8 - - - -
106B TRP 5.5 0.2 - - - -
107B PHE* 3.3 16.2 - - - +
108B SER* 3.0 33.7 + - - -
110B LYS* 1.3 76.9 - - - +
112B LEU* 1.3 60.8 + - - +
114B THR* 3.1 11.6 + - - -
115B VAL* 3.0 30.7 + - - +
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Residues in contact with LEU 112 (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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124A PHE* 4.0 5.6 - - + -
127A PHE* 4.6 2.7 - - + -
25B LEU* 5.6 3.8 - - + -
53B MET* 3.7 37.9 - - + -
87B LEU* 3.8 22.9 - - + -
107B PHE* 3.7 31.0 - - + +
108B SER 3.0 12.6 + - - +
109B GLU 3.4 8.7 - - - +
111B SER* 1.3 78.7 + - - +
113B ARG* 1.3 64.7 + - - +
115B VAL* 3.2 11.3 + - + +
116B PHE* 3.0 51.9 + - + -
126B ILE* 4.5 10.3 - - + -
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Residues in contact with ARG 113 (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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120A GLU* 2.7 49.6 + - - +
121A ASP* 2.9 29.3 + - - -
124A PHE* 3.6 29.1 - - + +
109B GLU* 2.9 50.7 + - - +
110B LYS* 3.5 16.3 - - + +
111B SER 3.4 0.4 - - - -
112B LEU* 1.3 70.7 - - - +
114B THR* 1.3 56.9 + - - +
116B PHE* 3.3 4.9 + - - +
117B ARG* 2.9 46.8 + - - +
167C ARG* 3.4 28.9 - - - +
170C ASP* 5.0 0.2 - - - -
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Residues in contact with THR 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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31B MET* 4.1 26.0 - - + -
110B LYS* 3.4 15.1 + - - +
111B SER* 3.1 12.4 + - - -
113B ARG* 1.3 73.0 - - - +
115B VAL* 1.3 60.2 + - - +
117B ARG* 3.5 17.9 + - + +
118B THR* 2.8 34.2 + - - +
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Residues in contact with VAL 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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25B LEU* 4.4 7.0 - - + -
28B TYR* 3.9 32.7 - - + -
31B MET* 4.0 13.6 - - + -
107B PHE* 4.0 19.3 - - + -
111B SER 3.0 19.3 + - - +
112B LEU* 3.2 16.8 + - + +
114B THR* 1.3 76.8 - - - +
116B PHE* 1.3 63.4 + - + +
118B THR* 3.2 5.6 + - - -
119B ASP* 2.9 25.8 + - - +
122B MET* 3.8 32.1 - - + -
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Residues in contact with PHE 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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120A GLU* 5.6 2.7 - - + +
123A ILE* 3.8 22.2 - - + -
124A PHE* 3.5 32.3 - + - -
127A PHE* 3.6 31.0 - + - -
112B LEU* 3.0 25.8 + - + +
113B ARG* 3.9 4.0 - - - +
115B VAL* 1.3 83.2 - - + +
117B ARG* 1.3 62.0 + - + +
118B THR 3.4 0.5 + - - -
119B ASP 3.7 4.9 - - - -
120B GLU* 3.4 23.6 + - - +
122B MET* 4.0 6.7 - - + -
123B ILE* 3.6 43.8 - - + +
126B ILE* 3.9 18.4 - - + -
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Residues in contact with ARG 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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120A GLU* 2.8 42.2 + - - +
113B ARG* 2.9 31.4 + - - +
114B THR* 3.7 17.5 + - + +
115B VAL 3.3 0.2 - - - -
116B PHE* 1.3 77.1 - - - +
118B THR* 1.3 56.9 - - - +
167C ARG* 3.8 4.8 - - - +
169C GLY* 3.2 28.1 + - - +
170C ASP* 3.0 42.0 + - - +
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Residues in contact with THR 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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28B TYR* 4.0 22.9 - - + +
31B MET* 3.6 18.7 - - + +
114B THR* 2.8 16.6 + - - +
115B VAL 3.2 8.4 + - - -
117B ARG* 1.3 78.0 - - - +
119B ASP* 1.3 62.5 + - + +
120B GLU 4.2 0.4 - - - -
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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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24B LYS* 5.7 0.3 - - - +
28B TYR* 3.0 34.1 + - + +
115B VAL 2.9 11.5 + - - +
116B PHE* 3.5 6.0 - - - +
118B THR* 1.3 82.3 - - + +
120B GLU* 1.3 66.6 + - - +
121B ASP* 3.2 12.5 - - - +
122B MET* 3.2 45.8 + - + +
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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