Contacts of the helix formed by residues 107 - 118 (chain B) in PDB entry 1F0K
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 VAL 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B MET* 4.6 2.2 - - + -
13B ALA 4.6 11.9 - - - +
14B GLY* 4.7 11.4 - - - +
40B LEU* 3.9 27.6 - - + +
41B GLY* 4.1 18.2 - - - +
42B THR* 4.2 9.0 - - + -
47B GLU* 5.4 1.3 - - - +
61B ILE* 3.6 32.3 - - + +
63B ILE* 3.8 15.6 - - + +
104B GLY 5.4 0.4 - - - +
105B GLY 4.9 2.9 - - - +
106B TYR* 1.3 77.0 - - - +
108B SER* 1.3 66.4 + - - +
109B GLY 3.1 1.2 + - - -
110B PRO* 3.4 6.7 - - - +
111B GLY* 3.2 16.6 + - - -
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Residues in contact with SER 108 (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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12B MET* 3.9 35.8 - - - +
102B GLY* 4.5 4.5 - - - -
104B GLY* 3.9 18.0 - - - -
105B GLY 2.6 20.4 + - - -
107B VAL* 1.3 79.3 - - - +
109B GLY* 1.3 58.0 + - - +
112B GLY* 2.7 30.8 + - - -
134B THR* 3.4 10.0 - - - +
135B ASN* 4.6 0.7 + - - -
138B LEU* 3.4 15.3 - - - +
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Residues in contact with GLY 109 (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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74B LEU* 5.4 0.7 - - - -
81B ILE* 5.7 0.2 - - - -
106B TYR 3.1 8.2 + - - -
108B SER* 1.3 80.9 + - - +
110B PRO* 1.3 68.6 - - - +
112B GLY* 3.8 0.3 - - - -
113B LEU* 3.0 28.2 + - - +
134B THR* 3.6 9.3 - - - +
137B TRP* 3.6 31.3 - - - -
138B LEU* 4.2 1.1 - - - +
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Residues in contact with PRO 110 (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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61B ILE* 4.1 8.1 - - + -
63B ILE* 4.2 11.7 - - + -
66B LEU* 5.0 3.1 - - + -
74B LEU* 5.5 6.5 - - + -
81B ILE* 4.0 17.7 - - + -
84B ALA* 3.8 39.5 - - + -
85B TRP* 4.1 6.1 - - - +
88B ALA* 3.9 3.5 - - - +
106B TYR 3.3 14.1 - - - +
107B VAL* 3.4 6.5 - - - +
109B GLY* 1.3 87.8 - - - +
111B GLY* 1.3 56.3 + - - +
113B LEU* 3.3 11.3 + - + +
114B ALA* 2.9 30.8 + - - +
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Residues in contact with GLY 111 (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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12B MET* 3.5 22.0 - - - -
40B LEU* 4.0 13.0 - - - +
61B ILE* 4.9 0.2 - - - +
88B ALA* 4.0 9.8 - - - +
92B MET* 3.3 10.5 - - - +
107B VAL 3.2 10.5 + - - -
109B GLY 3.2 0.6 - - - -
110B PRO* 1.3 80.3 - - - +
112B GLY* 1.3 61.2 + - - +
114B ALA 3.1 1.7 + - - -
115B ALA* 3.0 20.1 + - - +
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Residues in contact with GLY 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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12B MET* 3.6 13.5 - - - -
108B SER 2.7 22.5 + - - -
109B GLY 3.8 0.7 - - - -
111B GLY* 1.3 72.1 - - - +
113B LEU* 1.3 56.2 + - - +
115B ALA* 3.3 2.0 + - - +
116B TRP* 2.9 31.4 + - - +
122B VAL* 3.8 12.5 - - - +
138B LEU* 3.8 17.3 - - - -
141B ILE* 4.0 1.3 - - - +
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Residues in contact with LEU 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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71B ILE* 4.7 10.8 - - + -
75B ILE* 5.5 3.8 - - + -
81B ILE* 4.6 20.2 - - + -
85B TRP* 3.2 26.1 + - + +
109B GLY 3.0 23.0 + - - +
110B PRO* 3.7 5.8 - - + +
112B GLY* 1.3 76.7 - - - +
114B ALA* 1.3 62.3 + - - +
116B TRP* 3.9 20.6 - - + +
117B SER* 3.1 19.4 + - - -
137B TRP* 3.8 25.6 - - + -
141B ILE* 3.9 20.1 - - + +
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Residues in contact with ALA 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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85B TRP* 3.5 13.0 - - + +
88B ALA* 3.5 23.6 - - + -
89B ARG* 3.6 20.6 - - + +
92B MET* 4.1 5.6 - - - -
110B PRO 2.9 17.4 + - - +
111B GLY 3.5 4.7 - - - +
113B LEU* 1.3 75.2 - - - +
115B ALA* 1.3 65.4 + - - +
117B SER* 2.8 17.4 + - - -
118B LEU* 3.1 14.9 + - - +
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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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92B MET* 3.6 18.6 - - - -
100B VAL* 3.9 18.6 - - + -
111B GLY 3.0 15.2 + - - +
112B GLY* 3.7 4.7 - - - +
114B ALA* 1.3 73.9 - - - +
116B TRP* 1.3 65.8 + - - +
118B LEU* 3.0 8.5 + - - -
120B ILE* 2.9 36.7 + - + +
122B VAL* 3.7 17.0 - - + -
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Residues in contact with TRP 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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112B GLY 2.9 17.8 + - - +
113B LEU* 3.9 28.0 - - + +
115B ALA* 1.3 76.9 - - - +
117B SER* 1.3 75.8 + - - +
119B GLY* 3.0 14.8 + - - -
120B ILE 3.9 8.0 + - - -
122B VAL* 4.2 5.8 - - + +
141B ILE* 3.7 50.5 + - + +
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Residues in contact with SER 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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85B TRP* 3.4 22.0 + - - -
89B ARG* 2.8 29.4 + - - -
113B LEU 3.1 16.2 + - - -
114B ALA* 2.8 19.4 + - - -
116B TRP* 1.3 86.5 - - - +
118B LEU* 1.3 55.9 + - - +
119B GLY 3.3 0.8 + - - -
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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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89B ARG* 3.3 50.7 - - + +
92B MET* 3.7 29.6 - - + -
93B LYS* 4.0 20.9 - - + +
114B ALA 3.1 16.8 + - - +
115B ALA 3.0 6.7 + - - +
117B SER* 1.3 76.3 - - - +
119B GLY* 1.3 60.4 + - - +
120B ILE* 3.3 17.0 + - + +
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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