Contacts of the helix formed by residues 111 - 123 (chain B) in PDB entry 2FI2
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B LEU* 3.5 8.3 - - - +
109B PRO* 3.2 3.7 + - - +
110B GLY* 1.3 81.1 - - - +
112B PRO* 1.4 70.2 - - - +
113B GLU* 3.4 2.2 - - - -
114B GLU* 3.1 24.8 + - - +
115B ALA* 3.0 24.3 + - - +
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Residues in contact with PRO 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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62A LEU* 3.4 32.4 - - + +
85B GLU* 3.4 45.8 - - + +
86B LEU* 5.3 0.7 - - + -
88B VAL* 4.4 5.4 - - + -
89B LEU* 3.6 27.3 - - + +
92B PHE* 4.2 0.4 - - + -
110B GLY 4.6 0.7 - - - +
111B SER* 1.4 87.3 - - - +
113B GLU* 1.3 57.1 + - + +
115B ALA* 3.2 4.0 + - - +
116B ALA* 2.8 33.4 + - - +
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Residues in contact with GLU 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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59A GLN* 3.7 21.0 - - + +
62A LEU* 3.7 18.2 - - + -
66A ARG* 5.0 6.8 + - - -
85B GLU* 4.4 12.5 - - - +
111B SER* 3.4 2.1 - - - +
112B PRO* 1.3 78.7 - - + +
114B GLU* 1.3 59.7 + - - +
116B ALA* 3.4 4.4 - - - +
117B ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 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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109B PRO* 3.4 23.1 - - + +
111B SER* 3.1 26.9 + - - +
113B GLU* 1.3 76.7 - - - +
115B ALA* 1.4 63.7 + - - +
117B ALA* 3.1 13.6 + - - +
118B LEU* 2.9 40.5 + - + +
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Residues in contact with ALA 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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89B LEU* 3.7 6.3 - - + -
92B PHE* 3.8 7.6 - - + -
93B LEU* 3.5 32.1 - - + -
104B VAL* 4.6 2.2 - - + -
109B PRO* 3.7 11.0 - - + +
111B SER 3.0 13.3 + - - +
112B PRO 3.4 8.5 - - - +
114B GLU* 1.4 76.1 - - - +
116B ALA* 1.3 60.8 + - - +
118B LEU* 3.1 14.7 + - - +
119B VAL* 3.0 27.0 + - - +
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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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58A PRO* 3.3 16.3 - - + +
59A GLN* 3.4 31.2 - - + -
62A LEU* 3.7 6.3 - - + -
92B PHE* 3.7 2.9 - - + -
112B PRO 2.8 17.1 + - - +
113B GLU 3.4 9.4 - - - +
115B ALA* 1.3 74.2 - - - +
117B ALA* 1.3 52.0 + - - +
119B VAL* 3.1 12.1 - - - +
120B ASP* 2.7 36.8 + - - +
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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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59A GLN* 4.8 6.0 - - - +
113B GLU 2.9 14.9 + - - +
114B GLU* 3.1 19.7 + - - +
116B ALA* 1.3 74.7 - - - +
118B LEU* 1.3 65.6 + - + +
120B ASP* 3.6 16.4 + - - +
121B GLY* 3.8 4.2 + - - -
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Residues in contact with LEU 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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103B ARG 6.0 0.7 - - - +
104B VAL* 4.0 20.2 - - + -
107B GLN* 3.4 30.7 - - - +
109B PRO* 3.6 35.0 - - + -
114B GLU* 2.9 45.2 + - + +
115B ALA* 3.1 8.3 + - - +
117B ALA* 1.3 78.8 - - - +
119B VAL* 1.3 65.2 + - + +
121B GLY* 3.5 2.8 + - - -
122B LEU* 3.2 25.9 + - + +
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Residues in contact with VAL 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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52A TYR* 3.7 10.5 - - + +
58A PRO* 3.4 23.1 - - + -
92B PHE* 3.7 7.4 - - + -
96B LEU* 3.6 19.7 - - + -
100B ILE* 3.3 29.6 - - + +
104B VAL* 3.7 10.3 - - + -
115B ALA 3.0 15.5 + - - +
116B ALA* 3.1 15.3 - - - +
118B LEU* 1.3 73.3 - - - +
120B ASP* 1.3 58.7 + - - +
121B GLY 3.1 2.9 - - - -
122B LEU* 2.9 8.1 + - + +
123B ARG* 2.9 34.8 + - - +
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Residues in contact with ASP 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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58A PRO* 4.2 6.6 - - + +
59A GLN* 5.2 7.4 + - - +
116B ALA 2.7 22.6 + - - +
117B ALA* 3.6 13.6 - - - +
119B VAL* 1.3 72.4 - - - +
121B GLY* 1.3 55.8 + - - +
123B ARG* 2.7 48.6 + - - +
124B ARG* 2.8 50.5 + - - +
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Residues in contact with GLY 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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117B ALA 3.8 3.8 + - - -
118B LEU 3.5 6.9 + - - -
119B VAL 3.1 0.6 - - - -
120B ASP* 1.3 79.9 + - - +
122B LEU* 1.3 59.4 + - - +
123B ARG 3.2 0.7 - - - -
124B ARG* 3.0 41.8 + - - +
125B GLU 5.1 0.3 - - - +
128B GLY* 5.7 4.3 - - - -
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Residues in contact with LEU 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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100B ILE* 3.7 37.4 - - + +
103B ARG* 3.4 40.4 - - + +
104B VAL 5.0 0.2 - - - +
118B LEU* 3.2 23.3 + - + +
119B VAL* 2.9 12.5 + - + +
121B GLY* 1.3 76.6 - - - +
123B ARG* 1.3 60.1 + - - +
124B ARG 3.1 1.2 + - - -
125B GLU 5.8 0.2 - - - -
126B PRO* 3.8 25.8 - - - +
127B GLY 6.1 0.2 - - - +
128B GLY* 3.6 38.4 - - - +
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Residues in contact with ARG 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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52A TYR* 3.6 18.2 - - - +
54A GLU* 2.7 62.3 + - + +
55A ALA 5.0 0.8 + - - -
57A GLY* 3.3 11.3 - - - +
58A PRO* 3.6 16.7 - - - +
100B ILE* 4.8 5.4 - - + +
119B VAL 2.9 10.9 + - - +
120B ASP* 2.7 44.2 + - - +
122B LEU* 1.3 76.2 - - - +
124B ARG* 1.3 60.9 + - + +
125B GLU 3.0 7.9 + - - -
126B PRO* 5.0 2.5 - - - +
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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