Contacts of the helix formed by residues 112 - 128 (chain L) in PDB entry 1FQV
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 ILE 112 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L GLN* 4.0 13.0 - - + +
24L SER* 3.7 30.5 - - - -
58L VAL* 3.3 34.1 - - + -
61L TRP* 4.2 10.1 - - + -
62L CYS* 3.9 14.8 - - - -
107L ALA* 2.8 15.0 + - - +
110L LEU* 3.7 13.7 - - + +
111L ASP* 1.3 73.3 - - - +
113L LYS* 1.3 64.3 + - - +
114L GLY 3.0 3.8 + - - +
115L LEU* 3.7 24.9 - - + +
116L LEU* 2.9 24.2 + - - +
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Residues in contact with LYS 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L GLN 5.2 0.2 + - - -
25L VAL* 6.0 0.2 - - - +
111L ASP* 3.7 9.3 + - - +
112L ILE* 1.3 72.5 - - - +
114L GLY* 1.3 65.0 + - - +
116L LEU* 3.8 12.5 - - + +
117L ASP* 3.0 47.7 + - - +
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Residues in contact with GLY 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L TRP* 3.2 23.3 - - - -
112L ILE* 3.0 3.8 + - - +
113L LYS* 1.3 83.3 - - - +
115L LEU* 1.3 60.6 + - - +
117L ASP* 3.3 17.2 - - - +
118L VAL* 3.5 8.8 + - - +
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L VAL* 5.1 12.8 - - + -
61L TRP* 3.2 58.0 - - + +
92L PHE* 4.1 11.2 - - + -
93L LEU* 5.0 0.4 - - + -
103L LEU* 4.0 14.8 - - + +
107L ALA* 3.2 28.5 - - + +
112L ILE* 3.1 15.6 + - + +
114L GLY* 1.3 71.5 - - - +
116L LEU* 1.3 61.9 + - - +
117L ASP 3.1 1.8 - - - -
118L VAL* 3.3 10.3 - - + +
119L THR* 2.9 42.7 + - + +
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Residues in contact with LEU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K LEU* 4.6 9.6 - - + -
119K GLY* 6.2 0.4 - - - -
104L ILE* 4.4 13.0 - - + +
107L ALA* 3.9 18.3 - - + +
108L ASN* 3.9 30.3 - - - +
111L ASP* 5.3 5.6 - - - +
112L ILE 2.9 17.6 + - - +
113L LYS* 3.8 14.6 - - + +
115L LEU* 1.3 78.8 - - - +
117L ASP* 1.3 56.4 + - - +
119L THR* 3.1 11.7 + - - +
120L CYS* 2.8 53.8 - - - -
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Residues in contact with ASP 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K CYS* 4.4 4.4 - - - -
113L LYS* 3.0 33.6 + - - +
114L GLY* 3.3 13.9 - - - +
115L LEU 3.1 0.2 - - - -
116L LEU* 1.3 75.5 - - - +
118L VAL* 1.3 67.0 + - - +
120L CYS* 3.3 6.2 + - - +
121L LYS* 2.9 70.6 + - - +
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Residues in contact with VAL 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L TRP* 3.8 12.1 - - + +
85L ILE* 3.8 21.5 - - + +
86L PRO* 4.8 4.3 - - + -
89L ASP* 3.5 20.6 - - - +
93L LEU* 4.1 12.3 - - + -
114L GLY 3.6 12.3 - - - +
115L LEU* 3.3 30.3 - - + +
117L ASP* 1.3 79.7 - - - +
119L THR* 1.3 55.2 + - - +
121L LYS* 3.3 7.0 + - + +
122L THR* 2.5 42.1 + - - +
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Residues in contact with THR 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L LEU* 4.2 14.8 - - + -
100L LEU* 4.4 5.0 - - + +
103L LEU* 4.2 18.2 - - + -
104L ILE* 3.5 26.6 - - - +
115L LEU* 2.9 44.5 + - + +
116L LEU* 3.1 11.3 + - - -
118L VAL* 1.3 76.2 - - - +
120L CYS* 1.3 59.9 + - - +
122L THR* 3.3 8.6 - - - -
123L VAL* 3.1 32.6 + - - +
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Residues in contact with CYS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K LEU* 5.1 1.8 - - - -
119K GLY* 4.4 5.6 - - - -
120K ILE* 4.2 33.0 - - - +
123K CYS* 3.5 22.6 - - - +
104L ILE* 4.5 10.1 - - - -
116L LEU* 2.8 46.2 - - - +
117L ASP* 3.3 3.5 + - - +
118L VAL 3.2 0.4 - - - -
119L THR* 1.3 81.9 + - - +
121L LYS* 1.3 60.8 + - - +
123L VAL* 3.3 5.0 + - - +
124L ALA* 2.9 26.0 + - - +
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Residues in contact with LYS 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K CYS* 3.7 21.1 - - + +
85L ILE* 4.0 20.4 - - + -
117L ASP* 2.9 52.6 + - - +
118L VAL* 3.8 6.1 - - + +
120L CYS* 1.3 72.2 - - - +
122L THR* 1.3 61.4 + - - +
124L ALA* 3.3 9.6 - - + +
125L ASN* 2.8 36.4 + - - +
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Residues in contact with THR 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L ILE* 3.6 14.1 - - - +
93L LEU* 3.1 30.5 - - + +
100L LEU* 4.0 25.4 - - + -
118L VAL 2.5 24.4 + - - -
119L THR* 3.3 9.4 - - - -
121L LYS* 1.3 78.4 - - - +
123L VAL* 1.3 61.9 + - - +
125L ASN* 3.3 7.3 + - - +
126L MET* 3.1 30.1 + - + +
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Residues in contact with VAL 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K TRP* 4.1 10.8 - - + -
120K ILE* 3.8 25.6 - - + -
139K TRP* 6.3 1.3 - - + -
100L LEU* 3.6 21.1 - - + -
104L ILE* 3.4 23.3 - - + -
119L THR 3.1 14.2 + - - +
120L CYS 3.6 8.1 - - - +
122L THR* 1.3 76.9 - - - +
124L ALA* 1.3 65.0 + - - +
126L MET* 3.3 11.9 + - - +
127L ILE* 3.2 22.1 + - + +
139L PHE* 3.8 21.5 - - + -
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Residues in contact with ALA 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K ILE* 4.6 2.9 - - - +
123K CYS* 3.9 18.8 - - + +
124K LEU* 3.5 27.2 - - + +
120L CYS 2.9 13.7 + - - +
121L LYS* 3.1 15.0 + - + +
123L VAL* 1.3 73.1 - - - +
125L ASN* 1.3 69.4 - - - +
126L MET 3.0 1.8 - - - -
127L ILE* 2.9 17.0 + - - +
128L LYS* 2.9 20.3 + - - +
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Residues in contact with ASN 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L ILE* 4.1 17.5 - - - +
121L LYS* 2.8 21.5 + - - +
122L THR* 3.6 7.6 - - - +
124L ALA* 1.3 78.3 - - - +
126L MET* 1.3 60.8 + - + +
128L LYS* 3.4 45.3 + - - +
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Residues in contact with MET 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L LEU 5.4 3.4 - - - +
95L VAL 5.3 7.9 - - - +
97L GLN* 5.6 9.4 - - + +
100L LEU* 3.2 36.8 - - + -
122L THR* 3.1 20.6 + - + +
123L VAL* 3.3 11.7 - - - +
124L ALA 3.0 0.6 - - - -
125L ASN* 1.3 79.3 - - + +
127L ILE* 1.3 62.0 + - - +
128L LYS 3.4 6.4 - - - +
130L LYS* 3.3 31.2 - - - +
139L PHE* 3.7 30.5 - - + -
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Residues in contact with ILE 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K ILE* 4.7 6.7 - - + -
121K PHE* 5.4 0.2 - - + -
124K LEU* 4.4 19.3 - - + -
128K GLU* 4.7 2.0 - - + -
131K LYS* 2.5 28.7 + - + +
132K VAL* 3.7 28.9 - - + -
139K TRP* 4.2 18.6 - - + -
123L VAL* 3.3 21.8 - - + +
124L ALA* 2.9 7.3 + - - +
126L MET* 1.3 74.9 - - - +
128L LYS* 1.3 61.9 + - - +
130L LYS* 3.1 13.9 + - - +
135L ILE* 3.3 28.3 - - + -
139L PHE* 3.7 20.6 - - + -
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Residues in contact with LYS 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K CYS 4.4 11.9 + - - -
124K LEU* 4.5 1.2 - - - +
125K CYS* 3.7 37.2 - - - +
128K GLU* 3.5 22.4 + - + +
131K LYS* 3.4 7.2 - - - +
124L ALA* 2.9 19.8 + - - +
125L ASN* 3.4 40.5 - - - +
126L MET 3.4 7.7 - - - +
127L ILE* 1.3 77.8 - - - +
129L GLY* 1.3 58.3 + - - +
130L LYS* 3.2 4.0 + - - +
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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