Contacts of the helix formed by residues 113 - 123 (chain K) 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 PRO 113 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K SER 3.8 4.7 - - - +
112K LEU* 1.3 104.6 - - + +
114K ASP* 1.3 65.7 + - - +
115K GLU* 3.1 11.2 - - + +
116K LEU* 3.1 34.6 + - + +
117K LEU* 3.2 10.0 + - - +
138K ARG* 3.6 0.9 + - - +
105L LEU* 4.5 5.8 - - + -
108L ASN* 4.9 4.9 - - - +
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Residues in contact with ASP 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K PRO* 1.3 73.1 - - - +
115K GLU* 1.3 74.5 + - - +
116K LEU 3.4 0.7 + - - -
117K LEU* 3.6 2.4 + - - +
118K LEU* 3.3 29.7 + - + +
138K ARG* 2.6 40.2 + - - +
141K ARG* 3.9 13.2 + - - -
142K LEU* 3.4 27.3 - - + +
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Residues in contact with GLU 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K PRO* 3.1 9.1 - - + +
114K ASP* 1.3 97.0 + - - +
116K LEU* 1.3 66.6 + - + +
118K LEU* 3.8 12.4 - - + +
119K GLY* 3.5 13.7 + - - -
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Residues in contact with LEU 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K LEU* 3.5 23.1 - - + -
113K PRO* 3.1 36.1 + - + +
115K GLU* 1.3 81.5 - - + +
117K LEU* 1.3 64.9 + - - +
118K LEU 3.1 1.8 - - - -
119K GLY* 3.0 4.0 + - - +
120K ILE* 2.9 27.0 + - - +
104L ILE* 4.7 7.4 - - + +
105L LEU* 4.1 7.4 - - + -
108L ASN* 2.8 57.4 - - + +
116L LEU* 4.6 16.2 - - + -
120L CYS* 5.1 2.4 - - - -
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Residues in contact with LEU 117 (chain K).
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* 5.0 6.1 - - + +
112K LEU* 4.1 20.9 - - + +
113K PRO 3.2 12.2 + - - +
114K ASP 4.1 1.6 - - - +
116K LEU* 1.3 75.9 - - - +
118K LEU* 1.3 51.5 + - - +
120K ILE* 3.0 12.1 + - + +
121K PHE* 2.7 51.2 + - + -
138K ARG* 3.4 35.9 - - - +
139K TRP* 3.5 46.2 - - + +
142K LEU* 3.6 24.7 - - + -
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Residues in contact with LEU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ASP* 3.3 18.1 + - + +
115K GLU* 3.8 12.3 - - + +
117K LEU* 1.3 77.8 - - - +
119K GLY* 1.3 53.5 + - - +
121K PHE* 3.5 4.2 - - + +
122K SER* 2.7 36.8 + - - -
142K LEU* 3.4 42.2 - - + +
145K ASP* 3.4 33.7 - - + +
147K SER* 4.0 10.5 - - - +
148K LEU* 3.9 13.2 - - + +
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Residues in contact with GLY 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K GLU 3.5 8.5 + - - -
116K LEU* 3.0 8.7 + - - -
118K LEU* 1.3 79.1 - - - +
120K ILE* 1.3 59.8 + - - +
122K SER* 2.5 26.7 + - - -
123K CYS* 3.4 9.9 + - - -
116L LEU* 6.2 0.7 - - - -
120L CYS* 4.4 11.4 - - - -
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Residues in contact with ILE 120 (chain K).
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* 4.7 4.5 - - + -
112K LEU* 3.4 33.4 - - + -
116K LEU 2.9 9.1 + - - +
117K LEU* 3.4 15.3 - - + +
119K GLY* 1.3 75.7 - - - +
121K PHE* 1.3 65.8 + - + +
123K CYS* 3.0 24.8 + - - +
124K LEU* 3.7 7.2 + - + +
139K TRP* 6.1 1.6 - - + -
104L ILE* 4.4 15.5 - - + -
120L CYS* 4.2 32.5 - - + +
123L VAL* 3.8 27.6 - - + -
124L ALA* 4.8 2.5 - - - +
127L ILE* 4.7 11.2 - - + -
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Residues in contact with PHE 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K LEU* 2.7 35.8 + - + +
118K LEU* 3.6 5.2 - - + +
120K ILE* 1.3 77.5 - - + +
122K SER* 1.3 55.8 + - - +
123K CYS 2.9 5.8 - - - -
124K LEU* 2.8 42.3 + - + +
129K LEU* 4.0 12.9 - - + +
132K VAL* 4.1 7.6 - - + -
139K TRP* 3.4 76.9 - + + -
142K LEU* 4.0 17.3 - - + -
143K ALA* 3.8 24.2 - - + -
148K LEU* 3.9 15.0 - - + -
427K ARG* 4.3 2.1 + - - -
127L ILE* 5.4 0.2 - - + -
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Residues in contact with SER 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K LEU 2.7 18.3 + - - -
119K GLY* 2.5 24.8 + - - -
121K PHE* 1.3 72.8 - - - +
123K CYS* 1.3 61.3 + - - +
124K LEU 3.2 3.4 + - - +
148K LEU* 3.8 9.6 - - - +
427K ARG* 3.8 36.7 + - - +
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Residues in contact with CYS 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K GLY 3.4 15.3 - - - -
120K ILE 3.0 10.2 + - - +
121K PHE 2.9 1.0 - - - -
122K SER* 1.3 83.5 + - - +
124K LEU* 1.3 59.2 + - - +
125K CYS 4.0 0.9 + - - -
117L ASP* 4.4 5.6 - - - -
120L CYS* 3.5 25.4 - - - +
121L LYS* 3.7 29.3 - - + +
124L ALA* 3.9 22.1 - - + +
128L LYS* 4.4 7.4 + - - -
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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