Contacts of the helix formed by residues 107 - 116 (chain D) in PDB entry 5JRE
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 ASP 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C PRO* 5.4 2.1 - - + +
71C MET* 3.5 20.0 - - + +
73D TYR* 2.7 31.6 + - - -
101D LYS* 4.4 0.9 - - - +
106D VAL* 1.3 78.6 - - - +
108D THR* 1.3 64.0 + - - +
109D TRP* 2.9 9.5 + - - +
110D VAL* 2.7 36.0 + - - +
111D TYR* 3.1 19.5 + - - +
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Residues in contact with THR 108 (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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8C LEU* 4.0 22.7 - - + -
11C GLU* 4.0 9.2 - - + +
12C TYR* 4.2 17.3 - - - +
15C LEU* 3.7 21.9 - - + +
101D LYS* 3.1 33.2 + - - +
107D ASP* 1.3 74.9 - - - +
109D TRP* 1.3 63.1 + - - +
111D TYR* 3.4 3.0 + - - +
112D LEU* 3.1 36.8 + - + +
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Residues in contact with TRP 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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12C TYR* 3.9 27.8 - + - -
15C LEU* 4.0 17.1 - - + +
16C GLU* 3.7 24.9 - - - -
19C LYS* 4.9 5.6 - - + -
71C MET* 3.8 35.8 + - + +
72C PHE* 3.8 33.8 - + - -
73D TYR* 4.3 1.1 - + - +
77D PHE* 3.7 25.0 - + - -
107D ASP* 2.9 8.9 + - - +
108D THR* 1.3 76.1 - - - +
110D VAL* 1.3 65.9 + - - +
111D TYR 3.3 0.3 + - - -
112D LEU* 3.3 4.6 + - - +
113D PHE* 3.2 49.1 + + - -
159D ASN* 3.8 26.2 - - + -
162D LEU* 4.9 2.2 - - + -
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Residues in contact with VAL 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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73D TYR* 3.6 10.5 - - + +
77D PHE* 3.3 37.4 - - + +
80D LEU* 4.1 32.1 - - + +
81D GLN* 4.5 4.1 - - - +
84D VAL* 3.9 12.5 - - + +
106D VAL* 3.6 30.3 - - + -
107D ASP* 2.7 21.5 + - - +
109D TRP* 1.3 72.7 - - - +
111D TYR* 1.3 63.7 + - - +
113D PHE* 3.4 2.1 + - - +
114D GLY* 3.0 21.0 + - - -
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Residues in contact with TYR 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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2C LEU* 4.2 5.5 - - + +
3C PRO* 4.0 12.7 + - - +
8C LEU* 4.0 38.8 - - + +
84D VAL* 3.9 13.3 - - + +
98D ILE* 3.9 10.6 - - - +
99D PRO 2.7 30.1 + - - -
100D SER* 3.7 3.5 - - - -
101D LYS* 3.5 35.9 - - + -
104D LEU* 4.3 9.4 - - + -
106D VAL* 4.0 4.5 - - + -
107D ASP 3.1 18.3 + - - +
108D THR* 3.5 4.7 - - - +
109D TRP 3.2 0.2 - - - -
110D VAL* 1.3 81.9 - - - +
112D LEU* 1.3 64.3 + - + +
114D GLY* 3.3 1.0 + - - -
115D ILE* 2.8 57.7 + - + +
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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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2C LEU* 5.1 2.0 - - + -
8C LEU* 4.1 16.6 - - + -
12C TYR* 3.5 43.7 - - + -
108D THR* 3.1 27.9 + - + +
109D TRP* 3.3 4.7 + - - +
111D TYR* 1.3 80.5 - - + +
113D PHE* 1.3 60.4 + - - +
115D ILE* 3.8 4.0 - - + +
116D GLY* 2.9 26.9 + - - -
152D LEU* 4.6 14.5 - - + +
155D ILE* 4.0 25.1 - - + -
157D LEU* 4.6 6.3 - - + -
162D LEU* 4.0 22.4 - - + +
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Residues in contact with PHE 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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77D PHE* 3.6 32.8 - + + -
81D GLN* 3.5 13.7 + - + -
109D TRP* 3.2 56.5 + + - +
110D VAL 3.8 2.5 - - - +
112D LEU* 1.3 79.6 - - - +
114D GLY* 1.3 60.1 + - - +
116D GLY 3.5 5.2 + - - -
117D ASP* 3.4 18.9 - - - +
159D ASN* 3.5 23.8 - - - -
161D ASP* 3.7 27.1 - - + -
162D LEU* 3.6 24.0 - - + -
165D LYS* 3.7 22.1 - - - +
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Residues in contact with GLY 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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81D GLN* 3.5 29.1 - - - +
84D VAL* 4.0 11.2 - - - -
85D GLU* 3.8 5.0 - - - +
110D VAL 3.0 14.1 + - - -
111D TYR 3.7 2.2 - - - -
113D PHE* 1.3 74.6 - - - +
115D ILE* 1.3 64.4 + - - +
117D ASP* 3.0 19.0 + - - +
118D ILE* 3.7 8.8 + - - +
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Residues in contact with ILE 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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2C LEU* 3.7 26.0 - - + -
84D VAL* 4.0 4.7 - - + +
88D ALA* 4.1 17.9 - - + -
98D ILE* 3.6 29.8 - - + -
99D PRO* 5.6 0.2 - - + -
111D TYR* 2.8 56.0 + - + +
112D LEU* 3.9 6.1 - - + +
114D GLY* 1.3 71.6 - - - +
116D GLY* 1.3 59.5 + - - +
117D ASP 3.0 5.4 + - - -
118D ILE* 3.2 25.1 + - + +
119D ALA 4.8 0.2 + - - -
148D LEU* 3.9 19.0 - - + +
152D LEU* 4.7 7.6 - - + -
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Residues in contact with GLY 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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112D LEU 2.9 17.7 + - - -
113D PHE 3.8 0.2 - - - -
114D GLY 3.2 0.8 - - - -
115D ILE* 1.3 76.6 - - - +
117D ASP* 1.3 63.4 + - - +
118D ILE 3.7 0.4 - - - -
119D ALA 5.1 0.2 + - - -
152D LEU* 5.0 13.2 - - - -
165D LYS* 3.7 29.0 - - - +
168D TYR* 3.7 18.5 - - - -
169D VAL* 4.4 6.6 - - - +
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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