Contacts of the helix formed by residues 128 - 137 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126K VAL* 3.6 3.9 - - + +
127K THR* 1.3 77.7 - - - +
129K VAL* 1.3 64.3 + - - +
130K GLU* 3.3 15.9 - - - +
131K TRP* 3.3 22.3 + - - +
132K LEU* 3.2 24.0 + - + +
184K SER* 2.5 24.7 + - - +
185K GLN* 3.3 18.7 + - - +
142O THR* 3.8 22.9 + - - +
144O GLU* 5.0 3.1 + - - +
145O GLN* 3.5 21.8 + - - +
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Residues in contact with VAL 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K VAL* 3.7 13.9 - - + +
127K THR 3.7 0.6 - - - -
128K ASN* 1.3 76.8 - - - +
130K GLU* 1.3 63.4 + - - +
132K LEU* 3.0 8.0 + - + +
133K LEU* 2.9 46.4 + - + +
149K VAL* 4.5 1.1 - - + -
155K ASN* 3.3 26.7 + - - +
158K LYS* 3.8 30.3 - - + +
159K MET* 3.7 36.1 - - + -
162K LEU* 4.7 3.4 - - + -
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Residues in contact with GLU 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K THR 4.5 5.1 - - - +
128K ASN* 3.8 18.7 - - - +
129K VAL* 1.3 82.3 + - - +
131K TRP* 1.3 51.2 - - - +
133K LEU* 4.0 12.3 + - - +
134K ASP* 3.4 4.9 + - - +
146K TYR* 4.9 0.5 + - - -
150K ARG* 5.8 6.7 - - + +
155K ASN* 5.4 3.3 + - - +
158K LYS* 5.6 9.9 + - - +
154N THR* 5.6 1.3 + - - +
157N SER* 5.6 7.2 - - - +
160N ARG* 1.9 57.8 + - - +
144O GLU* 4.7 17.5 - - + +
145O GLN* 5.1 0.7 - - - +
148O ALA* 5.7 1.9 - - - +
165O PHE* 4.7 10.8 - - - -
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Residues in contact with TRP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K ASN* 3.3 23.9 + - - +
129K VAL 3.2 0.2 - - - -
130K GLU* 1.3 79.0 - - + +
132K LEU* 1.3 66.9 + - + +
133K LEU 3.2 0.2 - - - -
134K ASP* 3.2 14.0 + - + +
135K ALA* 3.3 20.3 + - + -
180K ALA* 3.3 30.7 - - + -
183K GLU* 3.4 34.1 - - + -
184K SER* 3.5 24.7 - - - -
120N ALA* 4.6 15.9 + - + +
123N ILE* 4.8 3.6 - - + +
124N ALA* 4.3 12.2 - - + +
160N ARG* 2.5 32.9 - - - +
144O GLU* 3.8 27.3 + - + -
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Residues in contact with LEU 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K VAL* 5.0 5.6 - - + -
128K ASN* 3.2 24.7 + - + +
129K VAL* 3.0 14.5 + - - +
131K TRP* 1.3 80.5 - - + +
133K LEU* 1.3 60.9 + - - +
135K ALA* 3.5 2.6 + - - +
136K LEU* 3.2 29.9 + - + +
159K MET* 5.8 3.6 - - + -
162K LEU* 5.1 11.4 - - + -
177K LEU* 4.2 17.7 - - + -
180K ALA* 3.7 27.6 - - + +
181K LEU* 3.8 33.0 - - + -
184K SER* 3.7 28.9 - - - +
185K GLN* 5.5 0.4 - - - +
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Residues in contact with LEU 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K VAL* 2.9 25.1 + - + +
130K GLU* 4.2 10.5 - - - +
131K TRP 3.2 0.2 - - - -
132K LEU* 1.3 77.2 - - - +
134K ASP* 1.3 59.3 + - - +
136K LEU 3.7 0.7 - - - -
137K TYR* 3.0 29.8 + - - +
141K LEU* 3.7 25.9 - - + +
146K TYR* 3.5 22.1 - - + +
149K VAL* 3.7 37.5 - - + -
150K ARG* 3.7 28.7 - - + -
158K LYS* 5.9 1.6 - - + -
162K LEU* 3.7 17.5 - - + -
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Residues in contact with ASP 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K TRP* 3.2 6.5 + - + +
132K LEU 3.2 0.6 - - - -
133K LEU* 1.3 76.7 - - - +
135K ALA* 1.3 62.5 + - - +
137K TYR* 3.5 8.3 + - - +
146K TYR* 2.9 26.0 + - - -
119N ARG* 3.2 26.2 + - - +
120N ALA* 4.4 12.3 + - + +
123N ILE* 2.7 35.5 - - + +
160N ARG* 1.2 75.7 + - - +
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Residues in contact with ALA 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K TRP* 3.3 23.8 + - + +
132K LEU 3.9 4.5 - - - +
133K LEU 3.3 0.2 - - - -
134K ASP* 1.3 80.1 - - - +
136K LEU* 1.3 61.6 + - - +
137K TYR 3.6 2.4 + - - +
139K LYS* 4.0 22.0 + - - +
176K LEU* 4.4 4.1 - - + +
180K ALA* 3.9 27.8 - - + -
183K GLU* 5.6 1.6 - - - +
120N ALA* 4.6 12.5 - - + +
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Residues in contact with LEU 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K LEU* 3.2 28.8 + - + +
133K LEU* 3.7 0.9 - - - -
134K ASP 3.3 0.2 - - - -
135K ALA* 1.3 76.7 - - - +
137K TYR* 1.3 59.6 + - - +
139K LYS* 4.3 1.1 - - - -
140K VAL* 3.0 34.7 + - + +
141K LEU* 2.9 44.7 + - + -
162K LEU* 5.8 0.9 - - + -
169K TRP* 4.8 2.9 - - + -
173K CYS 4.6 2.7 - - - +
176K LEU* 3.8 23.6 - - + +
177K LEU* 3.8 46.4 - - + +
180K ALA* 3.9 20.4 - - + -
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Residues in contact with TYR 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K LEU 3.0 16.9 + - - +
134K ASP 3.7 10.7 - - - +
135K ALA 3.3 6.0 - - - +
136K LEU* 1.3 77.7 - - - +
138K GLY* 1.3 63.3 + - - +
139K LYS* 3.1 9.1 + - - +
141K LEU* 3.6 16.6 - - - -
142K THR* 5.0 0.2 - - - -
143K ASP* 3.7 30.2 - - + +
146K TYR* 3.7 25.4 - + + -
116N ASP* 5.9 2.5 - - - -
119N ARG* 2.4 46.3 - - + +
163N PHE 5.5 1.3 - - - -
166N THR* 5.5 1.5 + - - -
167N PRO* 3.2 31.7 - - + +
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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