Contacts of the helix formed by residues 114 - 126 (chain t) in PDB entry 5JPQ
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 114 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112t ILE 3.7 1.0 + - - -
113t ASP* 1.3 73.7 + - - +
115t THR* 1.3 56.3 + - - +
116t PRO* 3.4 0.4 - - - -
117t PHE* 2.8 6.2 + - - -
118t ARG* 2.5 40.3 + - - +
167t PHE* 3.5 37.5 + - - -
170t GLN* 3.4 23.4 + - - -
172t ILE* 3.1 31.9 - - - -
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Residues in contact with THR 115 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113t ASP* 2.4 37.0 + - - -
114t SER* 1.3 71.0 + - - +
116t PRO* 1.3 63.5 - - + +
118t ARG* 3.5 12.6 + - - +
119t GLU* 2.7 61.5 + - + +
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Residues in contact with PRO 116 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82t ARG* 3.6 33.0 + - + +
83t LYS 4.2 9.6 - - - +
84t THR* 3.8 20.4 - - + +
113t ASP 3.4 15.0 - - - +
114t SER 3.6 0.2 - - - -
115t THR* 1.3 100.8 - - + +
117t PHE* 1.3 60.5 + - + +
119t GLU* 3.5 10.9 - - + +
120t TRP* 3.0 27.0 + - - +
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Residues in contact with PHE 117 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73t PHE* 3.3 28.9 - - + -
75t TRP* 3.7 29.7 - + + -
80t ILE* 4.3 16.2 - - + -
82t ARG* 3.9 12.8 - - + -
84t THR* 3.5 21.8 - - - -
112t ILE* 5.7 4.0 - - + -
113t ASP 4.2 8.7 - - - -
114t SER 2.8 9.1 + - - +
116t PRO* 1.3 83.2 - - + +
118t ARG* 1.3 57.6 + - - +
120t TRP* 3.7 5.5 - - - +
121t TYR* 2.7 38.1 + - - +
167t PHE* 3.7 21.1 - - + -
172t ILE* 4.7 7.2 - - + -
190t ILE* 3.2 33.9 - - + -
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Residues in contact with ARG 118 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114t SER* 2.5 29.8 + - - +
115t THR* 3.5 11.6 + - - +
117t PHE* 1.3 73.6 - - - +
119t GLU* 1.3 64.0 + - - +
121t TYR* 3.9 1.4 - - - +
122t LYS* 3.0 24.9 + - - +
128t ASP* 2.9 47.0 + - - +
129t LEU* 4.4 4.8 - - + -
130t GLY* 3.8 17.6 - - - +
167t PHE* 3.6 19.3 + - + -
170t GLN* 4.1 24.7 + - - +
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Residues in contact with GLU 119 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115t THR* 2.7 46.5 + - + +
116t PRO* 3.5 10.0 - - - +
118t ARG* 1.3 74.6 - - - +
120t TRP* 1.3 61.1 + - - +
122t LYS* 3.4 12.7 - - - +
123t LEU* 3.3 20.1 + - - +
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Residues in contact with TRP 120 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78t GLU* 4.2 11.4 - - + -
80t ILE* 3.1 46.4 - - + +
82t ARG* 3.1 35.1 - - - +
116t PRO 3.0 18.3 + - - +
117t PHE* 3.7 5.8 - - - +
119t GLU* 1.3 73.8 - - - +
121t TYR* 1.3 85.8 + + + +
122t LYS 2.7 6.0 + - - -
123t LEU* 2.8 25.6 + - + +
124t HIS* 3.0 43.1 + + + +
125t TYR* 3.7 34.5 - + - -
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Residues in contact with TYR 121 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75t TRP* 4.6 13.5 - + + -
78t GLU* 4.7 3.8 - - + -
117t PHE 2.7 22.6 + - - +
118t ARG 3.9 0.4 - - - +
120t TRP* 1.3 85.2 - + + +
122t LYS* 1.3 59.9 + - - +
124t HIS 4.2 0.7 - - - -
125t TYR* 3.3 61.9 + + + +
126t GLY 3.8 0.2 + - - -
127t ILE* 3.4 29.3 - - + +
129t LEU* 3.2 42.2 - - + -
157t GLN* 3.0 36.9 + - - +
159t LEU* 3.1 28.6 - - + +
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Residues in contact with LYS 122 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118t ARG 3.0 17.3 + - - +
119t GLU* 3.4 10.3 - - - +
120t TRP 2.7 1.2 + - - -
121t TYR* 1.3 76.2 - - - +
123t LEU* 1.3 63.7 + - + +
126t GLY* 2.8 31.5 + - - -
127t ILE 3.5 15.5 + - - +
128t ASP* 4.1 28.3 + - + +
137t VAL* 5.7 12.6 - - + -
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Residues in contact with LEU 123 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119t GLU 3.3 9.3 + - - +
120t TRP* 2.8 23.2 + - + +
122t LYS* 1.3 80.1 - - + +
124t HIS* 1.3 76.1 + - + +
149t LYS* 3.1 29.3 + - - +
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Residues in contact with HIS 124 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120t TRP* 3.0 48.6 + + + +
123t LEU* 1.3 86.5 - - + +
125t TYR* 1.3 77.6 + + + +
149t LYS* 4.4 7.7 - - - +
152t LYS* 2.9 57.6 + - + +
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Residues in contact with TYR 125 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78t GLU* 2.7 22.7 + - - -
120t TRP* 3.7 22.5 - + - -
121t TYR* 3.3 40.6 + + + +
124t HIS* 1.3 92.2 + + + +
126t GLY* 1.3 64.2 + - - +
127t ILE* 3.6 21.6 - - + +
138t LEU* 4.6 0.5 - - - +
149t LYS* 3.4 29.0 - - - +
152t LYS* 3.9 27.8 - - + -
153t ARG* 4.0 7.6 - - - +
155t LYS* 4.4 5.9 + - + +
157t GLN* 2.8 44.5 + - + -
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Residues in contact with GLY 126 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122t LYS* 2.8 18.2 + - - -
123t LEU 4.6 0.6 - - - -
125t TYR* 1.3 78.8 - - - +
127t ILE* 1.3 62.9 + - - +
128t ASP 4.3 0.4 - - - -
136t THR* 3.1 29.8 - - - +
137t VAL* 3.5 21.8 + - - -
138t LEU* 4.1 8.7 - - - -
146t HIS* 6.0 0.2 - - - -
149t LYS* 4.6 5.6 - - - +
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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