Contacts of the helix formed by residues 125 - 133 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123G CYS 4.0 0.4 + - - -
124G LEU* 1.3 74.2 - - - +
126G LEU* 1.3 69.1 + - - +
127G PRO* 3.2 17.9 - - + -
128G GLU* 2.8 42.8 + - - +
129G LEU* 3.0 8.4 + - - -
427G ARG* 5.5 3.6 - - - +
428G LEU* 4.5 2.0 - - - -
429G THR 5.8 0.7 - - - +
128H LYS* 3.6 13.4 - - - +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G CYS* 1.3 73.5 - - - +
127G PRO* 1.3 69.7 - - + +
129G LEU* 3.1 14.2 + - + +
130G LEU* 3.1 16.3 + - + +
149G TRP* 3.6 37.0 - - + -
152G LEU* 4.2 5.2 - - + -
154G LEU* 3.7 29.8 - - + -
428G LEU* 3.8 25.4 - - + +
429G THR 3.3 30.1 + - - +
430G LEU* 3.7 13.5 - - + -
159H TRP* 3.9 14.1 - - + -
160H CYS* 4.5 3.6 - - - -
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Residues in contact with PRO 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G CYS* 3.2 24.2 - - + -
126G LEU* 1.3 94.5 - - + +
128G GLU* 1.3 64.2 + - - +
130G LEU* 3.5 4.0 + - - +
131G LYS* 3.2 20.3 + - - +
429G THR 4.3 6.7 - - - +
430G LEU* 4.5 8.7 - - + -
160H CYS* 3.8 23.3 - - - -
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G LEU* 3.6 22.2 - - + -
125G CYS* 2.8 36.0 + - - +
127G PRO* 1.3 81.2 - - - +
129G LEU* 1.3 66.3 + - - +
131G LYS* 3.0 42.2 + - - +
132G VAL* 3.1 19.4 + - - +
127H ILE* 5.1 0.9 - - + -
128H LYS* 3.5 39.3 + - + +
129H GLY 3.6 7.3 + - - -
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Residues in contact with LEU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G PHE* 4.0 20.9 - - + +
124G LEU* 4.0 8.4 - - + +
125G CYS 3.0 10.1 + - - +
126G LEU* 3.1 10.3 + - - +
128G GLU* 1.3 78.0 - - - +
130G LEU* 1.3 59.9 + - + +
132G VAL* 2.9 26.8 - - + +
133G SER* 3.2 9.9 + - - -
143G ALA* 3.6 33.9 - - + +
148G LEU* 3.7 25.1 - - + -
149G TRP* 3.7 27.1 - - + +
427G ARG* 4.8 3.6 - - - +
428G LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LEU* 3.1 14.3 + - + +
127G PRO 3.5 6.9 + - - +
129G LEU* 1.3 75.0 - - + +
131G LYS* 1.3 62.7 + - - +
133G SER* 2.7 23.2 + - - +
134G GLY* 4.2 1.0 + - - -
143G ALA* 5.8 0.7 - - + +
149G TRP* 4.0 27.6 - - + -
167G LEU* 5.7 1.6 - - + -
157H ASN* 3.3 38.3 + - + +
159H TRP* 3.3 24.7 - - + +
160H CYS* 3.3 39.7 - - + -
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Residues in contact with LYS 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G PRO 3.2 11.6 + - - +
128G GLU* 3.0 31.0 + - - +
130G LEU* 1.3 78.5 - - - +
132G VAL* 1.3 63.8 + - - +
134G GLY* 3.0 12.5 + - - -
127H ILE* 2.6 27.1 + - + -
128H LYS* 3.3 1.2 - - - +
129H GLY* 2.8 25.3 - - - +
130H LYS 2.7 21.2 + - - +
131H THR* 4.2 1.8 - - - +
132H PRO* 3.3 35.1 - - + +
135H ILE* 3.9 15.5 - - + -
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Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G PHE* 4.2 15.5 - - + -
124G LEU* 3.5 15.3 - - + -
128G GLU 3.3 9.4 - - - +
129G LEU* 2.9 38.1 - - + +
131G LYS* 1.3 70.8 - - + +
133G SER* 1.3 57.2 + - - +
134G GLY 2.8 12.9 + - - -
135G VAL* 2.9 29.9 + - - +
139G TRP* 3.5 27.3 - - + +
143G ALA* 4.3 0.4 - - + -
127H ILE* 3.1 36.3 - - + -
135H ILE* 4.2 2.7 - - + -
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Residues in contact with SER 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G LEU 3.2 4.9 + - - -
130G LEU* 2.7 28.2 + - - +
132G VAL* 1.3 81.1 - - - +
134G GLY* 1.3 56.5 + - - +
135G VAL 3.5 0.4 - - - -
139G TRP 4.1 0.4 - - - -
140G TYR* 2.9 50.2 + - - +
143G ALA* 3.4 29.2 - - - -
144G SER* 5.7 2.0 - - - -
145H PHE* 3.9 2.4 - - - -
153H VAL* 4.2 1.0 - - - +
157H ASN* 3.3 15.8 + - - -
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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