Contacts of the helix formed by residues 130 - 141 (chain G) in PDB entry 1XFB
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 GLY 130 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128G LEU 3.1 1.0 + - - -
129G ASP* 1.3 71.1 - - - +
131G LEU* 1.3 64.1 + - - +
132G SER 3.2 3.4 - - - -
133G GLU* 3.1 23.2 + - - +
134G ARG* 3.1 27.4 + - - +
126H GLN* 2.9 20.5 + - - +
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Residues in contact with LEU 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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109G VAL* 3.6 33.4 - - + +
127G GLY 3.7 7.4 - - - +
128G LEU* 3.1 22.2 + - + +
129G ASP 3.1 4.0 + - - -
130G GLY* 1.3 77.3 - - - +
132G SER* 1.3 57.5 + - - +
134G ARG* 3.2 22.2 + - + +
135G CYS* 2.8 42.8 + - - -
148G TRP* 4.4 4.0 - - + -
174G TYR* 4.0 29.4 - - + +
177G ILE* 4.0 29.4 - - + -
178G CYS* 4.8 0.2 - - - -
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Residues in contact with SER 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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128G LEU 4.9 0.2 + - - -
130G GLY 3.1 1.4 + - - -
131G LEU* 1.3 79.0 - - - +
133G GLU* 1.3 74.7 + - - +
135G CYS 3.3 0.7 + - - -
136G ALA* 3.0 19.8 + - - +
177G ILE* 3.5 20.0 - - - +
180G GLN* 3.5 14.2 + - - -
181G ASN* 2.9 30.6 + - - +
115H PRO* 6.5 0.7 - - - -
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Residues in contact with GLU 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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130G GLY* 3.1 28.0 + - - +
132G SER* 1.3 86.1 + - - +
134G ARG* 1.3 64.5 + - + +
136G ALA* 3.3 8.4 + - - +
137G GLN* 3.0 24.0 + - - +
126H GLN* 5.3 1.6 + - - +
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Residues in contact with ARG 134 (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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108G LYS 4.5 1.8 + - - -
109G VAL* 3.0 41.7 + - - +
110G ASP 5.1 0.4 + - - -
111G LYS* 3.7 24.3 - - - +
127G GLY 3.4 20.2 + - - -
129G ASP 4.4 4.0 - - - -
130G GLY* 3.1 20.3 + - - +
131G LEU* 3.5 15.3 - - + +
133G GLU* 1.3 75.4 - - + +
135G CYS* 1.3 60.5 + - - +
137G GLN* 3.1 9.0 + - - +
138G TYR* 2.8 63.1 + - + +
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Residues in contact with CYS 135 (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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107G ILE* 6.5 0.2 - - - -
109G VAL* 5.1 7.0 - - - -
131G LEU* 2.8 48.1 + - - +
132G SER 3.7 4.5 - - - +
134G ARG* 1.3 68.6 - - - +
136G ALA* 1.3 67.9 + - - +
137G GLN 3.0 0.3 + - - -
138G TYR* 3.0 6.3 + - - +
139G LYS* 2.8 26.2 + - - +
177G ILE* 4.8 0.4 - - - -
178G CYS* 4.0 30.1 - - - -
181G ASN* 3.7 21.8 - - + +
183G ILE* 3.6 16.4 - - + +
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Residues in contact with ALA 136 (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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132G SER 3.0 8.4 + - - +
133G GLU* 3.4 12.8 - - - +
135G CYS* 1.3 77.6 - - - +
137G GLN* 1.3 56.5 + - - +
139G LYS* 3.6 6.5 + - - +
140G LYS* 3.1 35.7 + - - +
181G ASN* 3.5 22.3 + - - +
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85G TYR* 4.6 1.8 + - - +
133G GLU 3.0 13.9 + - - +
134G ARG* 3.3 10.8 - - - +
135G CYS 3.0 0.2 - - - -
136G ALA* 1.3 73.5 - - - +
138G TYR* 1.3 71.4 + - + +
140G LYS* 2.9 37.1 + - - +
141G ASP* 2.9 51.0 + - - +
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Residues in contact with TYR 138 (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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81G HIS* 2.6 45.6 + + - +
84G LEU* 3.7 15.9 - - + +
85G TYR* 3.6 15.7 - - - -
107G ILE* 3.8 36.7 - - + +
108G LYS 4.9 1.3 + - - -
109G VAL* 4.0 21.5 - - + -
134G ARG* 2.8 59.3 + - + +
135G CYS* 3.6 7.4 - - - +
137G GLN* 1.3 76.1 - - + +
139G LYS* 1.3 62.0 + - - +
141G ASP* 2.9 15.0 + - - +
142G GLY 3.2 0.7 + - - -
143G ALA* 3.0 22.6 + - + +
183G ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 139 (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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15G GLU* 2.9 28.8 + - - -
19G ILE* 3.7 5.5 - - - +
135G CYS 2.8 19.8 + - - +
136G ALA* 3.6 6.7 - - - +
138G TYR* 1.3 71.3 - - - +
140G LYS* 1.3 60.5 + - - +
142G GLY* 2.9 22.0 + - - -
143G ALA 3.2 20.6 + - - +
144G ASP* 2.9 22.2 + - - +
181G ASN 4.0 10.1 - - - +
182G GLY* 2.7 32.4 + - - +
183G ILE* 3.9 9.8 - - + +
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Residues in contact with LYS 140 (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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136G ALA* 3.1 18.9 + - - +
137G GLN* 2.9 36.0 + - - +
139G LYS* 1.3 79.3 - - - +
141G ASP* 1.3 65.2 + - - +
142G GLY 3.4 0.6 + - - -
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Residues in contact with ASP 141 (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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84G LEU* 4.7 9.2 - - + +
85G TYR* 2.6 43.5 + - + +
95G VAL* 3.8 19.8 - - - +
137G GLN* 2.9 30.5 + - - +
138G TYR* 2.9 10.9 + - - +
140G LYS* 1.3 85.6 - - - +
142G GLY* 1.3 56.2 + - - +
143G ALA 3.7 0.2 - - - -
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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