Contacts of the helix formed by residues 170 - 185 (chain N) 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 170 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125J ARG* 4.5 2.4 - - - +
187J TYR* 4.6 16.6 + - - +
191J ASP* 3.4 41.6 + - + +
168N ALA 4.1 0.8 + - - -
169N TRP* 1.3 75.1 - - - +
171N TRP* 1.3 64.7 + - - +
172N THR* 3.7 16.8 + - - +
173N CYS* 3.2 21.0 + - - +
174N LYS* 3.3 29.4 + - - +
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Residues in contact with TRP 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N LEU* 3.6 34.1 + - + +
113N HIS* 3.2 45.3 - + + -
170N ASN* 1.3 77.7 - - - +
172N THR* 1.3 57.7 + - - +
173N CYS 3.1 1.8 + - - -
174N LYS* 4.4 17.1 - - - +
175N ASP* 2.9 35.0 + - - +
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Residues in contact with THR 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170N ASN* 3.3 15.6 + - - -
171N TRP* 1.3 76.5 - - - +
173N CYS* 1.3 59.1 + - - +
175N ASP* 3.1 16.6 - - - +
176N LEU* 4.4 9.7 - - - +
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Residues in contact with CYS 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J TYR* 5.7 5.6 - - - -
136N LEU* 4.6 5.9 - - - +
140N VAL* 3.9 21.5 - - + +
169N TRP* 3.6 23.2 - - - -
170N ASN* 3.2 34.3 - - - +
171N TRP 3.1 0.2 - - - -
172N THR* 1.3 83.1 - - - +
174N LYS* 1.3 67.5 + - - +
175N ASP 3.2 1.3 - - - -
176N LEU* 3.3 25.5 + - + +
177N LEU* 3.4 8.3 + - - +
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Residues in contact with LYS 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N LEU 3.2 25.9 + - - +
113N HIS* 5.8 0.2 - - - +
115N ILE* 3.5 18.8 - - + +
116N ASP* 3.0 33.5 + - - +
166N THR* 4.5 9.4 + - - +
169N TRP* 3.7 39.5 + - + -
170N ASN 3.3 27.9 + - - +
171N TRP* 3.8 19.0 + - - +
173N CYS* 1.3 78.6 - - - +
175N ASP* 1.3 56.3 + - - +
177N LEU* 3.3 5.8 + - - +
178N LEU 3.3 16.6 + - - -
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Residues in contact with ASP 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N LEU* 3.1 32.3 - - + +
171N TRP* 2.9 29.7 + - - +
172N THR* 3.1 17.9 - - - +
174N LYS* 1.3 74.1 - - - +
176N LEU* 1.3 67.4 + - - +
177N LEU 3.2 0.7 - - - -
178N LEU* 3.3 13.4 + - + +
179N GLN* 3.1 34.6 + - - +
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Residues in contact with LEU 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ALA* 4.4 7.4 - - + +
136N LEU* 3.8 23.6 - - + -
139N LYS* 3.8 46.4 - - + +
140N VAL* 5.3 1.8 - - + -
172N THR 4.4 9.6 - - - +
173N CYS* 3.3 20.4 + - + +
174N LYS 3.2 0.8 - - - -
175N ASP* 1.3 83.3 + - - +
177N LEU* 1.3 57.5 + - - +
179N GLN* 3.5 20.5 + - - +
180N ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N ILE* 3.7 25.6 - - + -
122N LEU* 5.6 1.6 - - + -
132N LEU* 4.2 6.7 - - + -
136N LEU* 3.8 33.2 - - + -
159N MET* 5.5 5.2 - - + -
162N LEU* 3.7 25.6 - - + -
163N PHE* 5.9 1.3 - - + -
169N TRP* 3.6 33.7 - - + -
173N CYS 3.4 5.7 + - - +
174N LYS 3.3 9.7 + - - +
175N ASP 3.2 0.4 - - - -
176N LEU* 1.3 77.1 - - - +
178N LEU* 1.3 60.5 + - - +
179N GLN 3.3 0.4 - - - -
180N ALA* 3.8 1.5 - - - +
181N LEU* 3.0 39.0 + - + +
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Residues in contact with LEU 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N LEU* 3.7 33.7 - - + -
114N PHE* 3.6 34.3 - - + -
115N ILE* 4.4 8.5 - - + +
174N LYS 3.3 7.0 + - - +
175N ASP* 3.3 19.5 - - + +
177N LEU* 1.3 79.2 - - - +
179N GLN* 1.3 57.7 + - + +
181N LEU* 3.4 3.7 + - + +
182N ARG* 3.0 72.5 + - - +
189N VAL* 4.2 7.4 - - + -
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Residues in contact with GLN 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175N ASP* 3.1 20.3 + - - +
176N LEU* 3.6 22.8 - - - +
177N LEU 3.3 0.4 - - - -
178N LEU* 1.3 75.8 - - + +
180N ALA* 1.3 57.8 + - - +
182N ARG* 3.3 12.1 + - - +
183N GLU* 3.0 40.2 + - - +
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Residues in contact with ALA 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N TRP* 3.3 9.4 - - + -
132N LEU* 3.7 21.5 - - + +
135N ALA* 3.9 27.1 - - + -
136N LEU* 3.9 6.7 - - + -
176N LEU 3.2 14.3 + - - +
177N LEU 3.8 4.5 - - - +
178N LEU 3.2 0.2 - - - -
179N GLN* 1.3 74.7 - - - +
181N LEU* 1.3 61.0 + - - +
183N GLU* 4.5 4.3 - - - +
184N SER* 3.1 28.9 + - - -
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N PHE* 5.0 3.6 - - + -
115N ILE* 4.1 13.0 - - + -
122N LEU* 4.0 24.5 - - + -
126N VAL* 4.2 23.6 - - + -
132N LEU* 3.8 28.3 - - + -
159N MET* 5.6 2.2 - - + -
177N LEU* 3.0 34.9 + - + +
178N LEU* 3.4 4.9 + - + +
179N GLN 3.3 0.2 - - - -
180N ALA* 1.3 78.6 - - - +
182N ARG* 1.3 57.3 + - - +
184N SER* 4.5 2.0 - - - +
185N GLN* 2.8 41.5 + - + +
186N SER 3.5 1.0 + - - -
188N LEU* 5.4 1.3 - - + -
189N VAL* 3.8 21.5 - - + +
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Residues in contact with ARG 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N PHE* 6.0 0.2 - - - -
178N LEU* 3.0 56.5 + - - +
179N GLN* 3.8 11.2 - - - +
180N ALA 3.3 0.2 - - - -
181N LEU* 1.3 74.1 - - - +
183N GLU* 1.3 62.6 + - + +
186N SER* 2.3 38.2 + - - +
189N VAL* 3.7 22.2 - - + +
193N GLU* 3.3 23.4 + - - -
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Residues in contact with GLU 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N TRP* 3.4 28.9 - - + -
179N GLN* 3.0 25.5 + - + +
180N ALA* 4.1 2.8 - - - +
182N ARG* 1.3 79.4 - - + +
184N SER* 1.3 61.5 + - - +
186N SER* 4.6 1.6 + - - -
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Residues in contact with SER 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N ASN* 2.5 38.0 + - - +
131N TRP* 3.5 19.2 - - - -
132N LEU* 3.7 9.1 - - - +
180N ALA 3.1 19.1 + - - -
181N LEU 4.1 1.6 - - - -
183N GLU* 1.3 80.6 - - - +
185N GLN* 1.3 74.7 + - - +
187N TYR* 5.3 1.0 - - - -
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Residues in contact with GLN 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N ARG 4.8 3.4 + - - -
126N VAL* 5.5 2.2 - - + -
127N THR* 4.4 14.8 + - - +
128N ASN* 3.3 19.6 + - - +
132N LEU* 5.8 0.7 - - + -
181N LEU* 2.8 29.1 + - + +
184N SER* 1.3 97.6 + - - +
186N SER* 1.3 63.8 + - - +
187N TYR* 3.1 57.4 + - + -
188N LEU* 3.8 41.6 - - + +
189N VAL* 4.9 2.0 - - + +
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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