Contacts of the helix formed by residues 118 - 126 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P PHE* 3.3 52.5 + + - +
115P ILE 4.0 3.6 - - - -
116P ASP 3.4 0.2 - - - -
117P GLN* 1.3 98.9 + - + +
119P ARG* 1.3 57.1 + - - +
120P ALA 3.3 2.5 - - - -
121P ALA* 3.2 10.8 + - + +
122P LEU* 2.9 31.3 + - + +
192P LEU* 3.3 54.1 + - + +
193P GLU* 5.2 0.6 - - - -
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Residues in contact with ARG 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ASP* 3.8 9.6 + - - -
137M TYR* 3.2 57.1 + - + -
143M ASP* 5.5 0.8 + - - -
146M TYR* 3.3 37.9 + - - -
115P ILE 3.8 8.9 + - - +
116P ASP* 3.9 17.3 - - - +
117P GLN 3.4 4.4 + - - -
118P HIS* 1.3 77.3 - - - +
120P ALA* 1.3 62.7 + - - +
123P ILE* 3.3 50.7 + - - +
160P ARG* 4.6 6.7 + - - +
163P PHE* 3.7 51.1 + - + +
164P SER* 5.7 0.4 - - - +
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Residues in contact with ALA 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 5.2 10.2 + - + +
134M ASP* 3.9 37.8 - - + +
135M ALA* 4.8 3.8 - - - +
117P GLN 5.2 0.2 + - - -
118P HIS 3.3 0.6 - - - -
119P ARG* 1.3 79.6 - - - +
121P ALA* 1.3 61.4 + - - +
123P ILE* 3.9 3.5 + - - +
124P ALA* 3.6 21.0 + - - +
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Residues in contact with ALA 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P HIS* 3.2 14.8 + - + +
120P ALA* 1.3 78.6 - - - +
122P LEU* 1.3 60.5 + - - +
123P ILE 3.2 0.7 - - - -
124P ALA* 3.5 1.7 + - - -
125P ARG* 3.0 42.9 + - - +
188P LEU* 5.4 0.6 - - - +
192P LEU* 4.2 29.2 - - + -
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P PHE* 4.4 9.6 - - + +
115P ILE* 4.1 33.9 - - + +
118P HIS* 2.9 20.0 + - + +
120P ALA 3.5 0.2 - - - -
121P ALA* 1.3 73.7 - - - +
123P ILE* 1.3 64.3 + - - +
125P ARG 4.3 0.4 - - - -
126P VAL* 3.2 43.1 - - + +
159P MET* 3.3 13.0 - - + +
163P PHE* 3.7 27.1 - - + -
177P LEU* 5.6 0.4 - - + -
181P LEU* 4.0 19.3 - - + -
188P LEU* 4.3 9.9 - - + -
189P VAL* 6.1 1.1 - - + -
192P LEU* 3.9 22.0 - - + -
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Residues in contact with ILE 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 6.3 0.4 - - + -
134M ASP* 3.4 24.2 - - - +
119P ARG* 3.3 44.7 + - - +
120P ALA 4.2 4.0 - - - +
121P ALA 3.2 0.6 - - - -
122P LEU* 1.3 80.7 - - - +
124P ALA* 1.3 64.8 + - + +
125P ARG 3.4 0.5 + - - -
126P VAL 4.2 4.0 + - - +
156P PRO* 3.3 43.1 - - + +
159P MET* 3.8 10.5 - - + +
160P ARG* 3.7 36.1 - - + +
163P PHE* 3.8 17.3 - - + -
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Residues in contact with ALA 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 4.9 16.6 - - + +
120P ALA 3.6 13.8 + - - +
121P ALA* 3.5 2.2 + - - -
123P ILE* 1.3 84.5 - - + +
125P ARG* 1.3 70.0 + - + +
126P VAL 3.8 1.8 - - - +
127P THR* 5.3 4.0 - - - +
156P PRO* 4.4 13.7 - - + +
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Residues in contact with ARG 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P ALA* 3.0 22.6 + - - +
124P ALA* 1.3 89.2 - - + +
126P VAL* 1.3 60.7 + - - +
127P THR* 3.7 10.8 + - - +
185P GLN* 4.8 2.8 + - - -
187P TYR* 6.2 1.4 - - - -
188P LEU* 3.3 39.2 - - + +
191P ASP* 3.7 23.5 + - - +
192P LEU* 3.3 31.1 - - - +
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Residues in contact with VAL 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P LEU* 3.2 38.4 + - + +
123P ILE 4.5 6.2 - - - +
124P ALA 3.8 1.4 - - - +
125P ARG* 1.3 76.9 - - - +
127P THR* 1.3 63.7 + - - +
128P ASN* 3.9 9.6 - - + +
129P VAL* 3.7 25.1 - - + +
132P LEU* 5.0 3.6 - - + -
155P ASN* 3.9 16.3 + - - +
156P PRO* 5.9 0.3 - - - +
159P MET* 3.9 17.2 - - + +
181P LEU* 4.2 18.8 - - + -
185P GLN* 5.3 3.4 - - - +
188P LEU* 3.7 21.8 - - + -
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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