Contacts of the helix formed by residues 125 - 133 (chain O) 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 CYS 125 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123O CYS 4.0 0.2 + - - -
124O LEU* 1.3 73.2 - - - +
126O LEU* 1.3 56.5 + - - +
127O PRO* 3.3 17.7 - - + -
128O GLU* 2.7 54.3 + - - -
129O LEU* 3.0 8.6 + - - -
427O ARG 5.7 2.7 - - - -
428O LEU* 5.0 1.8 - - - -
429O THR 5.8 0.9 - - - +
128P LYS* 3.4 13.7 - - - +
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Residues in contact with LEU 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O CYS* 1.3 70.9 - - - +
127O PRO* 1.3 70.4 - - + +
129O LEU* 3.2 6.4 + - + +
130O LEU* 3.1 29.9 + - + +
149O TRP* 3.6 37.2 - - + -
152O LEU* 4.3 4.0 - - + -
154O LEU* 3.7 20.4 - - + -
428O LEU* 3.9 25.6 - - + +
429O THR 3.2 30.8 + - - +
430O LEU* 3.6 22.9 - - + -
159P TRP* 3.9 11.7 - - + -
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Residues in contact with PRO 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O CYS* 3.3 20.6 - - + -
126O LEU* 1.3 94.5 - - + +
128O GLU* 1.3 72.3 + - - +
130O LEU* 3.2 4.7 + - + +
131O LYS* 3.0 21.3 + - - +
429O THR 4.4 3.1 - - - +
430O LEU* 4.2 13.2 - - + -
160P CYS* 4.0 22.4 - - - -
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Residues in contact with GLU 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124O LEU* 3.6 20.6 - - + -
125O CYS* 2.7 38.8 + - - +
127O PRO* 1.3 82.4 - - - +
129O LEU* 1.3 61.3 + - - +
131O LYS* 2.8 36.2 + - - +
132O VAL* 3.1 27.2 + - - +
127P ILE* 4.9 1.1 - - + -
128P LYS* 3.3 43.5 + - + +
129P GLY 3.4 4.0 + - - -
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Residues in contact with LEU 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O PHE* 4.1 20.0 - - + +
124O LEU* 4.0 8.5 - - + +
125O CYS 3.0 11.0 + - - +
126O LEU* 3.2 10.7 + - + +
128O GLU* 1.3 76.8 - - - +
130O LEU* 1.3 60.5 + - + +
132O VAL* 3.0 23.8 - - + +
133O SER* 3.2 9.7 + - - -
143O ALA* 3.6 29.1 - - + +
148O LEU* 3.7 26.0 - - + -
149O TRP* 3.7 33.7 - - + +
427O ARG* 5.1 2.2 - - - +
428O LEU* 4.2 20.4 - - + -
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Residues in contact with LEU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O LEU* 3.1 17.2 + - + +
127O PRO* 3.2 7.4 + - + +
129O LEU* 1.3 76.3 - - + +
131O LYS* 1.3 62.8 + - - +
133O SER* 2.6 23.4 + - - +
134O GLY 4.3 0.3 + - - -
143O ALA 5.9 0.2 - - - +
149O TRP* 4.1 26.5 - - + -
167O LEU* 5.7 1.6 - - + -
153P VAL* 5.2 0.2 - - - +
157P ASN* 3.2 40.2 + - + +
159P TRP* 3.4 34.3 - - + +
160P CYS* 3.7 27.4 - - + -
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Residues in contact with LYS 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O PRO 3.0 10.9 + - - +
128O GLU* 2.8 37.1 + - - +
130O LEU* 1.3 76.9 - - - +
132O VAL* 1.3 65.7 + - - +
134O GLY* 3.0 12.1 + - - -
127P ILE* 2.5 28.6 + - + -
128P LYS* 3.2 1.6 - - - +
129P GLY* 2.8 14.9 - - - +
130P LYS 2.7 22.4 + - - +
131P THR* 4.3 1.3 - - - +
132P PRO* 3.4 37.0 - - + +
135P ILE* 3.6 17.5 - - + -
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Residues in contact with VAL 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O PHE* 3.9 22.4 - - + -
124O LEU* 3.4 13.5 - - + -
128O GLU 3.1 10.7 + - - +
129O LEU* 3.0 27.4 - - + +
131O LYS* 1.3 71.1 - - - +
133O SER* 1.3 53.4 + - - +
134O GLY 2.6 17.0 + - - -
135O VAL* 2.7 29.8 + - - +
139O TRP* 3.6 21.6 - - + +
143O ALA* 4.2 2.7 - - + -
127P ILE* 3.1 42.8 - - + -
135P ILE* 4.3 0.9 - - + -
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Residues in contact with SER 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O LEU 3.2 4.6 + - - -
130O LEU* 2.6 29.4 + - - +
132O VAL* 1.3 80.8 - - - +
134O GLY* 1.3 55.8 + - - +
135O VAL 3.5 0.4 - - - -
139O TRP 4.0 0.4 - - - -
140O TYR* 2.9 51.5 + - - +
143O ALA* 3.5 28.0 - - - -
144O SER* 5.6 2.5 - - - -
145P PHE* 3.8 1.4 - - - -
153P VAL* 4.1 1.8 - - - +
157P ASN* 3.4 13.0 + - - -
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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