Contacts of the helix formed by residues 142 - 150 (chain G) in PDB entry 6N1H
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 THR 142 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ASN* 3.8 21.6 + - - +
131C TRP* 6.5 0.2 - - - -
183C GLU 5.6 1.3 - - - +
184C SER* 4.1 18.2 - - - +
137G TYR* 4.2 2.0 - - - -
138G GLY* 6.0 0.2 - - - -
140G VAL 3.4 7.3 + - - +
141G LEU* 1.3 76.5 - - - +
143G ASP* 1.3 54.6 + - - +
144G GLU* 3.7 14.6 + - - +
145G GLN* 3.0 28.6 + - - +
146G TYR* 2.6 34.0 + - - +
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Residues in contact with ASP 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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124F ALA 4.7 4.9 - - - +
156F PRO* 5.2 1.8 - - + -
137G TYR* 3.7 25.0 + - - +
142G THR* 1.3 74.8 - - - +
144G GLU* 1.3 64.8 + - - +
146G TYR* 4.0 12.5 - - - -
147G GLN* 3.2 49.0 + - - +
119J ARG* 5.5 0.7 + - - -
164J SER* 6.1 0.5 - - - -
167J PRO* 2.5 40.1 - - + +
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Residues in contact with GLU 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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128C ASN* 5.0 6.1 - - - +
130C GLU* 4.7 16.1 - - + +
131C TRP* 3.8 22.2 + - + -
124F ALA* 2.7 36.8 - - - +
154F THR* 4.3 5.2 - - - +
156F PRO* 3.6 31.4 - - + -
160F ARG* 4.4 14.0 + - - +
142G THR* 3.2 17.4 + - - +
143G ASP* 1.3 87.1 + - - +
145G GLN* 1.3 59.8 + - - +
147G GLN 4.0 0.2 + - - -
148G ALA* 3.5 21.3 + - - +
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Residues in contact with GLN 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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127C THR* 3.7 6.7 + - - -
128C ASN* 3.5 37.0 - - - +
130C GLU* 5.1 1.6 - - - +
185C GLN* 4.3 4.6 + - - -
187C TYR* 4.9 4.8 + - - -
140G VAL* 3.7 9.4 - - - +
141G LEU* 3.4 35.5 - - + +
142G THR* 3.0 21.2 + - - +
144G GLU* 1.3 79.0 - - - +
146G TYR* 1.3 63.3 + - - +
147G GLN 3.4 0.2 - - - -
148G ALA 3.5 0.6 + - - -
149G VAL* 3.3 28.1 + - - +
165G PHE* 3.7 46.1 - - + +
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Residues in contact with TYR 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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133G LEU* 3.5 39.3 - - + +
134G ASP* 2.9 23.5 + - - -
137G TYR* 3.7 26.9 - + + -
141G LEU* 4.6 8.5 - - + +
142G THR 2.6 21.0 + - - +
143G ASP* 3.9 15.5 - - - +
144G GLU 3.4 0.2 - - - -
145G GLN* 1.3 74.5 - - - +
147G GLN* 1.3 67.0 + - + +
149G VAL* 3.5 13.1 + - - +
150G ARG* 3.5 52.1 + - - +
119J ARG* 3.3 29.3 + - - -
160J ARG* 3.6 11.1 + - - +
164J SER* 6.4 1.6 - - - -
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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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124F ALA 5.9 0.6 + - - -
127F THR* 5.2 3.8 - - - +
153F PRO 4.5 3.1 - - - +
154F THR* 3.1 23.3 + - - +
155F ASN* 3.0 21.9 + - - +
156F PRO* 2.4 39.5 - - + +
143G ASP* 3.2 37.0 + - - +
144G GLU 4.6 0.7 - - - +
145G GLN 3.4 0.2 - - - -
146G TYR* 1.3 82.6 - - + +
148G ALA* 1.3 64.9 + - - +
149G VAL 3.5 0.2 + - - -
150G ARG* 3.5 21.4 + - - +
151G ALA* 4.9 0.9 - - - +
164J SER* 4.2 25.7 + - - +
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Residues in contact with ALA 148 (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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130C GLU* 5.7 2.2 - - - +
154F THR* 2.6 26.1 - - + +
144G GLU 3.5 13.9 + - - +
145G GLN 3.9 5.6 - - - +
146G TYR 3.3 1.0 - - - -
147G GLN* 1.3 76.6 - - - +
149G VAL* 1.3 61.7 + - - +
150G ARG 3.7 0.2 + - - -
151G ALA* 4.3 5.5 + - - +
152G GLU* 4.1 6.8 - - - +
161G LYS* 3.4 24.8 - - + +
165G PHE* 4.1 17.9 - - + -
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Residues in contact with VAL 149 (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 VAL* 4.5 1.8 - - + -
133G LEU* 3.7 36.6 - - + -
141G LEU* 5.2 3.4 - - + -
145G GLN 3.3 16.4 - - - +
146G TYR 3.5 7.3 + - - +
147G GLN 3.2 0.4 - - - -
148G ALA* 1.3 77.8 - - - +
150G ARG* 1.3 51.8 + - - +
151G ALA 2.7 28.4 + - - +
152G GLU* 4.5 0.9 - - - +
158G LYS* 3.3 39.6 - - + +
161G LYS* 3.7 24.0 - - + +
162G LEU* 4.3 5.4 - - + +
165G PHE* 3.9 11.0 - - + -
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Residues in contact with ARG 150 (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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153F PRO* 5.4 3.3 - - - +
130G GLU* 5.8 4.8 - - + +
133G LEU* 3.7 17.5 - - + -
146G TYR* 3.5 55.4 + - - +
147G GLN* 3.5 13.4 + - - +
148G ALA 3.4 0.8 - - - -
149G VAL* 1.3 70.8 - - - +
151G ALA* 1.3 60.3 + - - +
158G LYS* 4.5 16.0 - - - +
157J SER* 4.4 9.5 + - - -
160J ARG* 3.5 49.3 + - - +
161J LYS* 4.9 7.8 - - - +
164J SER* 5.3 4.6 - - - -
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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