Contacts of the helix formed by residues 108 - 117 (chain B) in PDB entry 5FWP
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.7 3.6 + - - +
101B ASN* 4.6 4.0 - - - -
107B LYS* 1.3 81.7 - - - +
109B GLY* 1.3 59.4 + - - +
110B THR* 2.9 31.6 + - - -
111B LYS* 3.3 22.8 + - - +
112B ALA* 4.1 1.2 + - - +
127B GLY 3.8 13.5 - - - -
130B GLY* 3.9 4.0 - - - -
1692B ATP 2.9 36.8 + - - -
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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
----------------------------------------------------------
53B LYS* 4.2 8.8 + - - -
101B ASN* 4.0 19.1 - - - -
108B SER* 1.3 68.3 - - - +
110B THR* 1.3 58.0 + - - +
111B LYS 3.1 1.3 - - - -
112B ALA* 3.2 12.7 + - - +
113B PHE* 2.8 30.0 + - - +
1692B ATP 2.8 18.1 + - - -
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Residues in contact with THR 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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49B ASP* 4.4 9.2 + - - +
53B LYS* 4.3 11.5 + - - +
108B SER* 2.9 16.6 + - - -
109B GLY* 1.3 78.4 - - - +
111B LYS* 1.3 58.2 + - - +
113B PHE* 3.3 6.6 + - - +
114B MET* 2.8 44.1 + - - +
125B MET* 3.9 26.2 - - + -
126B ILE 3.5 24.2 + - - +
127B GLY 4.1 8.3 - - - +
1692B ATP 3.5 12.0 + - - -
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Residues in contact with LYS 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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23A GLN* 2.8 35.6 + - - +
27A LEU* 6.1 0.4 - - - +
108B SER 3.3 16.3 + - - +
109B GLY 3.1 0.4 - - - -
110B THR* 1.3 74.6 - - - +
112B ALA* 1.3 59.9 + - - +
114B MET* 3.1 13.7 + - - +
115B GLU* 2.8 36.4 + - + +
127B GLY 4.2 11.0 - - - +
128B GLN* 3.1 42.6 + - + +
129B PHE 5.0 2.7 + - - -
2E VAL* 4.2 16.5 - - - +
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Residues in contact with ALA 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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108B SER 4.1 1.1 + - - +
109B GLY* 3.2 17.0 + - - +
111B LYS* 1.3 75.9 - - - +
113B PHE* 1.3 65.4 + - - +
115B GLU* 3.2 20.3 + - - +
116B ALA* 3.1 19.8 + - - +
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Residues in contact with PHE 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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53B LYS* 3.4 50.9 - - + -
56B TYR* 3.6 20.2 - + + -
57B GLU* 3.3 22.0 - - + -
91B ILE* 4.7 3.4 - - + -
109B GLY 2.8 17.0 + - - +
110B THR 3.5 4.3 - - - +
112B ALA* 1.3 75.6 - - - +
114B MET* 1.3 57.7 + - - +
116B ALA* 2.9 14.4 + - + +
117B LEU* 2.8 51.9 + - + +
125B MET* 3.4 31.2 - - + -
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Residues in contact with MET 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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110B THR* 2.8 42.8 + - + +
111B LYS* 3.4 12.3 - - - +
113B PHE* 1.3 73.6 - - - +
115B GLU* 1.3 63.9 + - - +
117B LEU* 3.1 31.8 + - + +
118B GLN* 3.2 15.3 + - - +
125B MET* 4.3 27.6 - - + +
126B ILE* 5.5 1.6 - - - -
127B GLY 5.8 1.8 - - - -
128B GLN* 6.6 0.2 - - - -
358B ARG* 5.2 8.7 - - - +
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Residues in contact with GLU 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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111B LYS* 2.8 22.5 + - + +
112B ALA* 3.3 20.1 - - - +
113B PHE 3.1 0.2 - - - -
114B MET* 1.3 76.0 - - - +
116B ALA* 1.3 60.9 + - - +
118B GLN* 3.1 45.1 + - - +
119B ALA 4.5 0.2 + - - -
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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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56B TYR* 3.9 17.2 + - + -
57B GLU* 5.5 2.5 - - - +
112B ALA 3.1 10.6 + - - +
113B PHE* 2.9 22.0 + - + +
115B GLU* 1.3 75.2 - - - +
117B LEU* 1.3 57.6 + - - +
118B GLN 3.1 4.6 + - - -
119B ALA* 3.4 19.4 + - - +
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Residues in contact with LEU 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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56B TYR* 3.5 42.2 - - + -
113B PHE* 2.8 34.7 + - + +
114B MET* 3.1 29.1 + - + +
116B ALA* 1.3 71.3 - - - +
118B GLN* 1.4 55.6 + - - +
119B ALA 3.1 5.8 - - - -
120B GLY* 3.1 24.2 + - - -
121B ALA* 3.6 15.1 + - + +
123B ILE* 3.5 34.5 - - + +
125B MET* 4.4 3.1 - - + +
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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