Contacts of the helix formed by residues 135 - 147 (chain G) in PDB entry 3Q2K
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 ASN 135 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131G GLN* 4.1 2.1 - - - +
132G ASN* 2.9 37.1 + - - +
134G ARG* 1.3 77.0 - - - +
136G ALA* 1.3 65.8 + - - +
137G THR* 3.6 7.2 - - - +
138G LEU* 3.9 7.0 - - + +
139G GLN* 3.0 21.1 + - - +
267G ALA 3.8 10.5 + - - -
268G VAL* 3.7 22.2 + - - +
293G THR* 3.5 28.3 - - + +
296G VAL* 5.7 4.5 - - - +
300G GLY* 6.0 1.6 - - - -
303G LEU* 5.8 1.8 - - - -
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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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134G ARG 3.1 6.1 + - - -
135G ASN* 1.3 71.4 - - - +
137G THR* 1.3 63.9 + - - +
139G GLN* 3.4 7.7 + - - +
140G LEU* 3.3 25.6 + - - +
289G ALA* 3.7 21.5 - - + +
292G GLU* 3.7 33.8 + - - +
293G THR* 3.0 13.0 + - - +
303G LEU* 6.0 0.2 - - - +
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Residues in contact with THR 137 (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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135G ASN* 3.6 2.3 - - - +
136G ALA* 1.3 74.9 - - - +
138G LEU* 1.3 66.0 + - - -
140G LEU* 3.4 5.5 + - - +
141G VAL* 3.4 21.5 + - - +
263G VAL* 4.2 5.6 - - - -
268G VAL 2.8 24.1 + - - -
269G ASN 3.9 14.6 - - - -
271G ILE* 4.1 16.6 - - + +
289G ALA* 3.7 14.1 - - - +
290G ASN* 3.4 24.9 - - - +
293G THR* 2.9 29.4 + - - +
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Residues in contact with LEU 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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132G ASN* 3.5 24.2 - - + +
133G ARG 5.2 0.2 - - - +
135G ASN* 3.3 10.3 + - + +
137G THR* 1.3 84.1 + - - +
139G GLN* 1.3 60.9 + - - +
141G VAL* 3.7 6.5 - - + +
142G LYS* 2.8 30.8 + - - +
195G LEU* 4.0 25.1 - - + -
198G TRP* 4.2 14.4 - - + -
199G LEU* 3.9 12.3 - - + +
252G ILE* 4.2 20.2 - - + -
263G VAL* 4.4 10.3 - - + -
268G VAL* 3.6 38.1 - - + -
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Residues in contact with GLN 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ARG 2.5 26.8 + - - +
134G ARG* 3.2 38.7 + - - +
135G ASN 3.0 20.7 + - - +
136G ALA* 3.8 8.7 - - - +
137G THR 3.4 0.2 - - - -
138G LEU* 1.3 75.4 - - - +
140G LEU* 1.3 61.0 + - + +
142G LYS* 3.4 8.6 + - - +
143G LYS* 2.9 49.1 + - + +
198G TRP* 4.0 14.5 - - - -
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ALA 3.3 11.9 + - - +
137G THR 3.7 5.6 - - - +
138G LEU 3.3 0.4 - - - -
139G GLN* 1.3 75.9 - - + +
141G VAL* 1.3 58.7 + - - +
143G LYS* 3.2 9.4 + - + +
144G ALA* 2.9 29.8 + - - +
271G ILE* 4.2 12.6 - - + -
274G TRP* 3.9 17.7 - - + -
282G ASP* 4.1 24.5 - - + +
285G LYS* 3.9 38.8 - - + +
286G ILE* 4.3 7.6 - - + -
289G ALA* 3.4 27.8 - - + -
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Residues in contact with VAL 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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137G THR 3.4 11.8 + - - +
138G LEU* 3.2 13.1 + - + +
140G LEU* 1.3 71.6 - - - +
142G LYS* 1.3 68.4 + - - +
143G LYS 3.1 0.2 + - - -
144G ALA* 3.1 5.0 + - - +
145G ILE* 2.9 31.4 + - + +
150G PHE* 5.0 4.7 - - + -
199G LEU* 4.2 14.8 - - + -
252G ILE* 5.8 0.7 - - + -
254G ILE* 3.8 28.9 - - + -
261G VAL* 3.8 27.8 - - + -
263G VAL* 3.9 15.7 - - + -
271G ILE* 4.9 0.9 - - + -
274G TRP* 4.0 13.7 - - + -
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Residues in contact with LYS 142 (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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138G LEU 2.8 17.8 + - - +
139G GLN* 3.6 13.5 - - - +
140G LEU 3.3 0.2 - - - -
141G VAL* 1.3 77.5 - - - +
143G LYS* 1.3 59.9 + - + +
145G ILE* 3.0 7.4 + - + +
146G GLU* 2.9 56.4 + - + +
198G TRP* 3.2 58.9 + - + +
199G LEU* 3.8 23.1 + - + +
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Residues in contact with LYS 143 (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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139G GLN* 2.9 40.6 + - - +
140G LEU* 3.6 7.4 - - + +
141G VAL 3.1 0.4 - - - -
142G LYS* 1.3 75.6 - - + +
144G ALA* 1.3 62.0 + - - +
146G GLU* 3.2 16.3 + - - +
147G GLN* 2.8 51.3 + - - +
282G ASP* 4.3 16.2 - - - +
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Residues in contact with ALA 144 (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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140G LEU 2.9 14.5 + - - +
141G VAL 3.7 6.5 - - - +
143G LYS* 1.3 75.8 - - - +
145G ILE* 1.3 63.7 + - - +
147G GLN* 3.5 11.5 + - - -
148G GLY 3.3 2.8 + - - -
149G ARG* 3.1 43.8 + - + +
150G PHE* 4.2 6.9 - - + -
274G TRP* 4.3 6.1 - - + -
276G PHE* 3.9 28.3 - - + -
282G ASP* 5.6 0.6 + - - -
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Residues in contact with ILE 145 (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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141G VAL* 2.9 27.8 + - + +
142G LYS* 3.0 9.4 + - + +
144G ALA* 1.3 76.4 - - - +
146G GLU* 1.3 59.7 + - + +
148G GLY* 3.1 17.4 + - - -
150G PHE* 3.6 25.4 - - + -
153G ILE* 4.4 17.3 - - + -
199G LEU* 2.9 54.1 - - + +
200G VAL* 4.4 7.9 - - + +
254G ILE* 4.5 9.0 - - + -
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Residues in contact with GLU 146 (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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142G LYS* 2.9 52.8 + - + +
143G LYS* 3.7 22.5 + - - +
145G ILE* 1.3 74.5 - - + +
147G GLN* 1.3 63.6 - - + +
148G GLY 3.0 6.0 + - - -
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Residues in contact with GLN 147 (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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143G LYS* 2.8 42.5 + - - +
144G ALA* 3.8 1.9 + - - -
145G ILE 3.4 0.2 - - - -
146G GLU* 1.3 77.2 - - + +
148G GLY* 1.3 62.5 + - - +
149G ARG* 3.2 34.2 + - + +
280G HIS* 3.6 30.3 + - + -
282G ASP* 4.3 4.3 + - - +
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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