Contacts of the helix formed by residues 118 - 126 (chain C) 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 HIS 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C PHE* 3.3 51.3 + + - +
115C ILE 4.0 3.8 - - - -
116C ASP 3.4 0.2 - - - -
117C GLN* 1.3 100.6 + - + +
119C ARG* 1.3 56.8 + - - +
120C ALA 3.3 3.1 - - - -
121C ALA* 3.2 9.4 + - + +
122C LEU* 2.9 31.7 + - + +
192C LEU* 3.3 53.3 + - + +
193C GLU* 5.2 0.8 - - - -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE 3.8 10.1 + - - +
116C ASP* 3.9 15.5 - - - +
117C GLN 3.4 4.2 + - - -
118C HIS* 1.3 77.3 - - - +
120C ALA* 1.3 63.9 + - - +
123C ILE* 3.3 46.6 + - - +
160C ARG* 4.6 11.9 + - - +
163C PHE* 3.7 51.8 + - + +
164C SER* 5.7 0.6 - - - +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLN 5.2 0.4 + - - -
118C HIS 3.3 0.2 - - - -
119C ARG* 1.3 82.0 - - - +
121C ALA* 1.3 61.7 + - - +
123C ILE* 3.9 7.3 + - - +
124C ALA* 3.6 21.5 + - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C HIS* 3.2 15.6 + - + +
120C ALA* 1.3 78.6 - - - +
122C LEU* 1.3 60.5 + - - +
123C ILE 3.2 0.4 - - - -
124C ALA* 5.1 1.8 - - - -
125C ARG* 3.0 42.5 + - - +
188C LEU* 5.4 0.7 - - - +
192C LEU* 4.2 28.9 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.4 9.6 - - + +
115C ILE* 4.1 33.9 - - + +
118C HIS* 2.9 20.6 + - + +
119C ARG 3.7 0.2 + - - -
121C ALA* 1.3 73.4 - - - +
123C ILE* 1.3 64.0 + - - +
125C ARG 4.3 0.2 - - - -
126C VAL* 3.2 43.3 - - + +
159C MET* 3.3 11.6 - - + +
163C PHE* 3.7 27.6 - - + -
177C LEU* 5.6 0.9 - - + -
181C LEU* 4.0 17.7 - - + -
188C LEU* 4.3 10.1 - - + -
189C VAL* 6.1 0.9 - - + -
192C LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.3 46.2 + - - +
120C ALA* 4.2 8.1 - - - +
121C ALA 3.2 0.6 - - - -
122C LEU* 1.3 80.9 - - - +
124C ALA* 1.3 63.8 + - + +
125C ARG 3.4 0.7 + - - -
126C VAL 4.2 3.8 + - - +
156C PRO* 3.3 42.5 - - + +
159C MET* 3.8 10.4 - - + +
160C ARG* 3.7 50.0 - - + +
163C PHE* 3.8 17.9 - - + -
144D GLU* 5.4 0.2 - - - +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ALA 3.6 13.5 + - - +
121C ALA* 3.5 2.9 + - - +
123C ILE* 1.3 80.5 - - + +
125C ARG* 1.3 70.2 + - + +
126C VAL 3.8 1.4 - - - +
127C THR* 5.3 1.9 - - - +
156C PRO* 4.4 9.8 - - - +
143D ASP* 4.7 5.5 - - - +
144D GLU* 2.8 30.3 - - - +
147D GLN* 5.8 1.0 + - - -
167G PRO* 3.9 12.5 - - - +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ALA* 3.0 21.3 + - - +
124C ALA* 1.3 90.2 - - + +
126C VAL* 1.3 53.4 + - - +
127C THR* 4.5 0.9 - - - -
188C LEU* 3.3 26.1 - - + +
191C ASP* 3.7 20.5 + - - +
192C LEU* 3.3 31.5 - - - +
167G PRO* 2.8 27.9 + - + +
168G ALA* 2.7 37.7 - - - +
169G TRP 2.9 31.9 + - - -
170G ASN* 4.3 0.8 - - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU* 3.2 39.6 + - + +
123C ILE 4.5 6.2 - - - +
124C ALA 3.8 0.9 - - - -
125C ARG* 1.3 76.1 + - - +
127C THR* 1.3 64.9 + - - +
128C ASN* 3.9 9.4 - - + +
129C VAL* 3.7 24.9 - - + +
132C LEU* 5.0 3.8 - - + -
155C ASN* 3.9 15.9 + - - +
156C PRO* 5.9 0.2 - - - +
159C MET* 3.9 17.2 - - + +
181C LEU* 4.2 18.4 - - + -
185C GLN* 5.3 3.4 - - - +
188C LEU* 3.6 21.8 - - + -
168G ALA* 4.4 0.4 - - - -
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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