Contacts of the helix formed by residues 128 - 137 (chain O) 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 ASN 128 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126O VAL* 3.6 4.2 - - + +
127O THR* 1.3 79.8 - - - +
129O VAL* 1.3 62.8 + - - +
130O GLU* 3.3 15.7 - - - +
131O TRP* 3.3 22.4 - - - +
132O LEU* 3.2 23.4 + - + +
184O SER* 2.5 29.1 + - - +
185O GLN* 3.3 19.5 + - - +
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Residues in contact with VAL 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O VAL* 3.7 13.9 - - + +
127O THR 3.7 0.6 - - - -
128O ASN* 1.3 78.3 - - - +
130O GLU* 1.3 62.3 + - - +
132O LEU* 3.0 8.0 + - - +
133O LEU* 2.9 46.6 + - + +
149O VAL* 4.5 0.9 - - + -
155O ASN* 3.3 27.1 + - - +
158O LYS* 3.8 30.5 - - + +
159O MET* 3.7 36.3 - - + -
162O LEU* 4.7 2.9 - - + -
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Residues in contact with GLU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O THR 4.5 5.0 - - - +
128O ASN* 3.8 18.3 - - - +
129O VAL* 1.3 82.1 + - - +
131O TRP* 1.3 59.8 + - + +
133O LEU* 4.0 12.4 + - - +
134O ASP* 3.0 27.4 + - - +
146O TYR* 4.9 1.7 + - - -
150O ARG* 5.8 7.6 - - - +
155O ASN* 5.4 3.1 + - - +
158O LYS* 5.6 9.4 + - - +
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Residues in contact with TRP 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O ASN* 3.3 24.5 + - - +
129O VAL 3.2 0.2 - - - -
130O GLU* 1.3 84.3 - - + +
132O LEU* 1.3 66.3 + - + +
133O LEU 3.2 0.4 - - - -
134O ASP* 3.2 21.5 + - + +
135O ALA* 3.3 18.7 + - + -
180O ALA* 3.3 31.4 - - + -
183O GLU* 3.4 33.2 - - + -
184O SER* 3.5 24.7 - - - -
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Residues in contact with LEU 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O VAL* 5.0 5.8 - - + -
128O ASN* 3.2 24.3 + - + +
129O VAL* 3.0 14.3 + - + +
131O TRP* 1.3 81.6 - - + +
133O LEU* 1.3 62.6 + - - +
135O ALA* 3.5 2.6 + - - +
136O LEU* 3.2 29.7 + - - +
159O MET* 5.8 3.4 - - + -
162O LEU* 5.1 11.0 - - + -
177O LEU* 4.2 17.9 - - + -
180O ALA* 3.7 26.9 - - + +
181O LEU* 3.8 31.4 - - + -
184O SER* 3.7 29.4 - - - +
185O GLN* 5.5 0.7 - - + +
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Residues in contact with LEU 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O VAL* 2.9 23.7 + - + +
130O GLU* 4.2 11.4 - - - +
131O TRP 3.2 0.4 - - - -
132O LEU* 1.3 76.6 - - - +
134O ASP* 1.3 59.5 + - - +
136O LEU* 3.4 1.2 + - - +
137O TYR* 3.0 29.3 + - - +
141O LEU* 3.7 25.4 - - + +
146O TYR* 3.5 22.1 - - + +
149O VAL* 3.7 38.4 - - + -
150O ARG* 3.7 28.7 - - + -
158O LYS* 5.9 1.8 - - + -
162O LEU* 3.7 18.4 - - + -
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Residues in contact with ASP 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O GLU 3.0 17.5 - - - +
131O TRP* 3.2 19.9 + - + +
133O LEU* 1.3 76.9 - - - +
135O ALA* 1.3 63.1 + - - +
137O TYR* 3.5 18.5 + - - +
146O TYR* 2.9 28.5 + - - -
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Residues in contact with ALA 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O TRP* 3.3 25.1 + - + +
132O LEU 3.5 4.2 + - - +
134O ASP* 1.3 79.9 - - - +
136O LEU* 1.3 61.7 + - - +
137O TYR 3.6 2.3 + - - +
139O LYS* 4.0 22.3 + - - +
176O LEU* 4.4 4.0 - - + +
180O ALA* 3.9 27.1 - - + -
183O GLU* 5.6 1.3 - - - +
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Residues in contact with LEU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O LEU* 3.2 28.0 + - + +
133O LEU 3.7 0.4 - - - -
134O ASP 3.3 0.4 - - - -
135O ALA* 1.3 76.5 - - - +
137O TYR* 1.3 59.5 + - - +
139O LYS* 4.3 1.3 - - - -
140O VAL* 3.0 34.5 + - + +
141O LEU* 2.9 46.0 + - + -
162O LEU* 5.8 1.8 - - + -
169O TRP* 4.8 4.0 - - + -
173O CYS 4.6 2.0 - - - +
176O LEU* 3.8 23.6 - - + +
177O LEU* 3.8 46.4 - - + +
180O ALA* 3.9 20.6 - - + -
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Residues in contact with TYR 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133O LEU 3.0 16.3 + - - +
134O ASP* 3.7 15.8 - - - +
135O ALA 3.3 5.8 - - - +
136O LEU* 1.3 78.2 - - - +
138O GLY* 1.3 63.3 + - - +
139O LYS* 3.1 9.2 + - - +
141O LEU* 3.6 16.8 - - - -
143O ASP* 3.7 45.3 + - + +
146O TYR* 3.7 30.5 - + + -
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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