Contacts of the helix formed by residues 108 - 119 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D THR 4.3 12.6 - - - -
52D SER* 4.4 4.1 + - - +
87D LEU* 4.0 2.0 - - - -
106D TRP 4.0 3.2 + - - -
107D PHE* 1.3 76.1 - - - +
109D GLU* 1.3 64.1 + - - +
110D LYS* 3.6 8.9 + - - +
111D SER* 3.0 35.8 + - - -
112D LEU* 3.1 9.9 + - - +
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Residues in contact with GLU 109 (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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9C ASP* 5.2 1.4 - - - +
124C PHE* 3.5 26.0 - - + +
128C LYS* 4.8 3.5 + - - -
51D THR 4.7 1.4 + - - -
87D LEU* 3.6 17.6 - - + +
88D TYR* 2.7 34.1 + - + +
108D SER* 1.3 73.8 - - - +
110D LYS* 1.3 57.7 + - - +
112D LEU* 3.2 6.6 + - - +
113D ARG* 3.0 60.9 + - - +
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Residues in contact with LYS 110 (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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108D SER* 3.3 7.9 + - - +
109D GLU* 1.3 77.3 + - - +
111D SER* 1.3 63.0 + - - +
113D ARG* 3.3 22.7 + - - +
114D THR* 3.4 15.1 + - - +
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Residues in contact with SER 111 (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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31D MET* 3.1 30.7 - - - +
32D GLY* 4.5 1.6 - - - -
107D PHE* 3.4 13.1 - - - +
108D SER* 3.0 35.0 + - - -
110D LYS* 1.3 79.4 - - - +
112D LEU* 1.3 55.0 + - - +
114D THR* 3.3 10.7 + - - -
115D VAL* 3.0 30.0 + - - +
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Residues in contact with LEU 112 (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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124C PHE* 4.1 4.3 - - + -
127C PHE* 4.8 2.0 - - + -
25D LEU* 5.8 3.1 - - + -
53D MET* 4.0 22.7 - - + -
87D LEU* 3.9 33.9 - - + -
107D PHE* 3.6 31.6 - - + +
108D SER 3.1 15.9 + - - +
109D GLU* 3.2 6.3 + - - +
111D SER* 1.3 76.6 + - - +
113D ARG* 1.3 66.1 + - - +
115D VAL* 3.1 10.0 + - + +
116D PHE* 2.9 53.3 + - + -
126D ILE* 4.4 12.3 - - + -
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Residues in contact with ARG 113 (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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120C GLU* 2.8 48.8 + - - +
121C ASP* 2.7 30.7 + - - +
124C PHE* 3.7 27.6 - - + +
109D GLU* 3.0 49.3 + - - +
110D LYS* 3.5 16.1 - - + +
112D LEU* 1.3 75.5 - - - +
114D THR* 1.3 56.7 + - - +
116D PHE* 3.3 5.3 + - - +
117D ARG* 2.9 52.8 + - - +
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Residues in contact with THR 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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31D MET* 3.7 28.5 - - + -
110D LYS* 3.4 11.4 + - - +
111D SER* 3.3 12.5 + - - -
112D LEU 3.3 0.2 - - - -
113D ARG* 1.3 73.7 - - - +
115D VAL* 1.3 61.5 + - - +
117D ARG* 3.5 16.2 + - + +
118D THR* 2.7 35.1 + - - +
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Residues in contact with VAL 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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25D LEU* 4.5 7.4 - - + -
28D TYR* 3.9 29.2 - - + -
31D MET* 3.9 19.3 - - + -
107D PHE* 4.0 21.5 - - + -
111D SER 3.0 21.7 + - - +
112D LEU* 3.1 14.3 + - + +
114D THR* 1.3 75.2 - - - +
116D PHE* 1.3 64.1 + - + +
118D THR* 3.0 7.8 + - - -
119D ASP* 2.9 24.8 + - - +
122D MET* 3.9 26.9 - - + -
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Residues in contact with PHE 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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120C GLU* 5.7 2.2 - - + +
123C ILE* 3.7 28.0 - - + -
124C PHE* 3.6 24.0 - + - -
127C PHE* 3.5 32.1 - + - -
112D LEU* 2.9 34.1 + - + +
113D ARG* 3.9 4.3 - - - +
115D VAL* 1.3 87.0 - - + +
117D ARG* 1.3 60.8 + - - +
118D THR 3.4 0.7 + - - -
119D ASP 3.5 10.9 + - - -
120D GLU* 3.5 16.1 + - - +
122D MET* 4.0 6.1 - - + -
123D ILE* 3.7 36.0 - - + +
126D ILE* 3.8 23.1 - - + -
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Residues in contact with ARG 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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120C GLU* 2.7 41.2 + - - +
113D ARG* 2.9 37.8 + - - +
114D THR* 3.7 15.7 + - + +
116D PHE* 1.3 74.3 - - - +
118D THR* 1.3 58.4 + - - +
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Residues in contact with THR 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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28D TYR* 3.8 22.7 - - + +
31D MET* 3.5 21.8 - - + +
114D THR* 2.7 19.4 + - - +
115D VAL 3.0 9.3 + - - -
117D ARG* 1.3 79.5 - - - +
119D ASP* 1.3 59.5 + - - +
120D GLU 4.2 0.9 - - - -
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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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24D LYS* 5.5 1.7 - - - +
28D TYR* 3.1 36.8 + - + +
115D VAL 2.9 10.5 + - - +
116D PHE* 3.5 7.5 + - - +
118D THR* 1.3 80.0 - - - +
120D GLU* 1.3 67.3 + - - +
121D ASP* 3.1 14.2 - - - +
122D MET* 3.2 46.4 + - + +
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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