Contacts of the helix formed by residues 114 - 126 (chain B) in PDB entry 1JFI
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 PRO 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.9 25.8 - - + -
16A ARG* 4.7 13.0 - - + +
112B THR 3.4 6.0 - - - +
113B ILE* 1.3 93.4 - - + +
115B ARG* 1.3 67.5 + - - +
116B ALA* 5.0 0.7 - - + -
117B ALA* 2.8 28.3 + - + +
118B ILE* 3.4 4.9 + - - +
718E A 4.2 28.9 - - - +
719E A 3.6 9.4 - - - +
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Residues in contact with ARG 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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113B ILE 3.4 2.6 + - - -
114B PRO* 1.3 70.5 - - - +
116B ALA* 1.3 63.8 + - - +
118B ILE* 3.1 3.8 + - - +
119B ASN* 2.9 41.1 + - - +
133B ASN* 3.3 46.9 + - - +
136B ARG* 4.0 17.3 - - - +
137B GLU* 3.2 37.0 + - - +
140B VAL* 4.2 20.2 - - + +
719E A 2.9 68.8 + - + +
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Residues in contact with ALA 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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114B PRO* 3.1 1.7 - - + +
115B ARG* 1.3 80.5 - - - +
117B ALA* 1.3 56.9 + - - +
119B ASN* 3.2 8.0 + - - +
120B LYS* 2.9 30.1 + - - +
718E A 3.6 21.8 - - - +
719E A 3.9 23.3 + - - +
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Residues in contact with ALA 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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10A ALA* 3.8 7.9 - - + +
11A ARG 4.7 7.0 - - - +
12A PHE* 3.7 29.1 - - + -
13A PRO* 5.1 3.4 - - + -
113B ILE* 3.7 6.1 - - + -
114B PRO* 2.8 20.3 + - + +
116B ALA* 1.3 77.6 - - - +
118B ILE* 1.3 61.4 + - - +
120B LYS* 3.4 7.6 + - - +
121B MET* 3.1 22.2 + - - +
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Residues in contact with ILE 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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12A PHE* 4.4 4.0 - - + -
46A LEU* 4.8 3.4 - - + -
113B ILE* 3.4 32.1 - - + -
114B PRO 3.8 4.7 - - - +
115B ARG* 3.1 7.7 + - - +
117B ALA* 1.3 79.3 - - - +
119B ASN* 1.3 67.8 + - - +
121B MET* 3.2 7.5 + - - +
122B ILE* 2.9 42.5 + - + +
136B ARG* 4.2 7.0 - - + +
139B VAL* 4.1 18.4 - - + -
140B VAL* 3.7 35.4 - - + -
143B CYS* 3.9 23.3 - - - -
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Residues in contact with ASN 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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115B ARG* 2.9 37.7 + - - +
116B ALA* 3.2 6.9 + - - +
118B ILE* 1.3 79.6 - - - +
120B LYS* 1.3 65.9 + - - +
122B ILE* 3.9 1.6 - - - +
123B LYS* 3.0 24.9 + - - +
136B ARG* 2.7 42.4 + - - +
719E A 4.3 15.6 - - - -
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Residues in contact with LYS 120 (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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10A ALA* 4.4 13.7 - - + +
11A ARG 6.1 0.2 - - - +
116B ALA 2.9 16.1 + - - +
117B ALA* 3.7 7.2 - - - +
119B ASN* 1.3 77.4 - - - +
121B MET* 1.3 57.5 + - - +
123B LYS* 3.5 5.3 + - + +
124B GLU* 3.0 65.1 + - + +
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Residues in contact with MET 121 (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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10A ALA* 3.6 33.8 - - + +
12A PHE* 4.6 5.8 - - + -
43A GLU* 4.1 27.1 - - + +
46A LEU* 4.1 25.6 - - + -
47A GLU* 5.1 4.5 - - + -
50A LEU* 4.3 6.1 - - + -
117B ALA 3.1 14.3 + - - +
118B ILE* 3.5 11.4 - - - +
119B ASN 3.2 0.2 - - - -
120B LYS* 1.3 73.8 - - - +
122B ILE* 1.3 64.9 + - - +
124B GLU* 3.2 13.6 + - + +
125B THR* 2.8 55.6 + - - +
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Residues in contact with ILE 122 (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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50A LEU* 3.8 30.7 - - + -
118B ILE* 2.9 34.4 + - + +
119B ASN 3.9 4.0 - - - +
121B MET* 1.3 76.2 - - - +
123B LYS* 1.3 55.4 + - - +
126B LEU* 2.7 45.9 + - + +
129B VAL 5.0 2.2 - - - +
131B VAL* 3.6 34.1 - - + -
136B ARG* 3.5 42.6 - - + +
139B VAL* 4.8 4.7 - - + -
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Residues in contact with LYS 123 (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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119B ASN 3.0 19.2 + - - +
120B LYS* 3.8 5.8 - - - +
122B ILE* 1.3 80.5 - - - +
124B GLU* 1.3 64.6 + - + +
126B LEU 4.6 5.4 - - - +
127B PRO* 3.6 23.4 - - + +
128B ASN* 5.5 12.5 - - - +
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Residues in contact with GLU 124 (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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10A ALA* 3.3 27.9 + - - +
120B LYS* 3.0 51.7 + - + +
121B MET* 3.8 9.8 - - + +
123B LYS* 1.3 77.6 - - + +
125B THR* 1.3 59.8 + - - +
127B PRO* 4.1 8.6 - - - +
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Residues in contact with THR 125 (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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47A GLU* 3.8 35.4 - - + +
50A LEU* 4.3 12.3 - - + +
51A LYS* 4.0 28.4 - - + +
121B MET* 2.8 40.9 + - - +
122B ILE 4.0 0.9 - - - -
124B GLU* 1.3 75.9 - - - +
126B LEU* 1.3 65.9 + - + +
127B PRO* 3.0 14.9 - - - +
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Residues in contact with LEU 126 (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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50A LEU* 4.0 37.7 - - + +
51A LYS* 4.4 7.4 - - + -
54A CYS* 3.9 27.1 - - + -
65A MET* 4.2 18.2 - - + -
122B ILE* 2.7 28.9 + - + +
123B LYS* 3.8 3.9 - - - +
125B THR* 1.3 85.7 - - + +
127B PRO* 1.3 66.2 - - - +
128B ASN 3.1 3.3 + - - -
129B VAL* 3.4 41.1 + - + +
131B VAL* 4.6 4.7 - - + -
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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