Contacts of the helix formed by residues 168 - 185 (chain A) in PDB entry 6NFJ
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 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASP 3.1 17.0 + - - +
104A GLY* 2.3 33.9 + - - +
105A LYS* 3.9 1.8 - - - +
157A ARG* 3.3 25.2 + - - +
158A LEU* 2.9 16.6 + - - +
160A PRO* 4.0 14.9 - - - +
166A VAL 4.9 1.2 - - - +
167A ALA* 1.3 76.6 - - - +
169A ALA* 1.3 66.2 + - - +
170A LYS 4.6 0.2 - - - +
171A GLY* 4.0 9.6 - - - +
172A LEU* 3.2 23.0 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA 3.6 2.5 + - - -
168A ASN* 1.3 75.7 - - - +
170A LYS* 1.3 83.0 + - + +
172A LEU* 4.1 3.3 - - - +
173A GLN* 3.3 29.1 + - - +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 3.2 50.4 + - + +
131A TYR* 3.6 7.3 + - - +
168A ASN* 4.6 0.6 - - - +
169A ALA* 1.3 90.0 - - + +
171A GLY* 1.3 65.6 + - - +
173A GLN* 3.2 28.0 + - - +
174A TYR* 3.3 9.5 + - - +
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 5.0 2.2 + - - +
131A TYR* 4.0 8.4 + - - -
157A ARG* 4.0 32.1 - - - -
158A LEU* 3.9 6.7 - - - -
168A ASN* 3.7 8.2 + - - +
169A ALA 3.4 0.6 - - - -
170A LYS* 1.3 78.1 - - - +
172A LEU* 1.3 61.6 + - - +
174A TYR* 3.3 8.3 + - - +
175A TYR* 3.1 22.9 - - - -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.0 8.7 - - + +
167A ALA* 4.4 8.5 - - + +
168A ASN 3.2 19.5 + - - +
169A ALA* 4.1 3.6 - - - +
171A GLY* 1.3 76.5 - - - +
173A GLN* 1.3 59.8 + - + +
174A TYR 3.4 0.2 + - - -
175A TYR* 3.6 1.5 + - - +
176A SER* 3.0 30.0 + - - -
224A TYR* 3.8 29.6 - - + +
228A MET* 4.3 13.9 - - + -
229A PHE* 3.5 34.3 - - + -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 3.3 22.3 + - - +
170A LYS* 3.2 21.0 + - - +
172A LEU* 1.3 75.6 - - + +
174A TYR* 1.3 54.4 + - - +
176A SER* 4.1 6.5 - - - -
177A THR* 2.7 45.2 + - + +
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.0 24.5 - - + +
130A SER* 2.9 41.3 + - - -
131A TYR* 3.3 53.2 - + + -
134A LEU* 4.0 31.3 - - + +
151A PHE* 5.9 0.2 - + - -
157A ARG* 4.9 0.2 - - - -
170A LYS 3.3 3.9 + - - +
171A GLY 3.3 9.5 + - - +
172A LEU 3.2 1.0 - - - -
173A GLN* 1.3 78.6 - - - +
175A TYR* 1.3 83.0 + + - +
177A THR* 3.1 6.7 + - - -
178A LEU* 2.9 40.2 + - + +
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.0 24.0 + - - -
151A PHE* 3.5 22.9 - + + -
152A SER 3.8 3.8 - - - -
153A ILE* 3.5 38.1 - - + -
154A SER* 2.8 29.1 + - - -
157A ARG* 3.8 14.6 - - + -
158A LEU* 3.9 18.2 - - + -
171A GLY 3.1 25.6 - - - -
172A LEU 3.6 1.5 + - - +
174A TYR* 1.3 89.4 - + - +
176A SER* 1.3 60.3 - - - +
178A LEU* 4.1 5.6 - - + -
179A LEU* 3.0 36.3 + - + +
229A PHE* 3.9 21.1 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.0 23.7 + - - -
173A GLN* 3.7 7.9 - - - -
174A TYR 3.2 0.2 - - - -
175A TYR* 1.3 74.9 - - - +
177A THR* 1.3 62.3 + - - +
179A LEU 3.4 0.9 + - - -
180A ASP* 2.9 40.9 + - - +
229A PHE* 4.6 7.8 - - - -
232A ARG* 3.6 22.2 + - - +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.3 11.4 - - - +
173A GLN* 2.7 32.1 + - + +
174A TYR* 3.1 11.3 + - - -
176A SER* 1.3 74.2 - - - +
178A LEU* 1.3 59.5 + - - +
180A ASP* 3.9 9.3 - - - +
181A ALA* 3.3 23.9 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.6 31.9 - - + -
138A LEU* 4.5 7.2 - - + -
141A LEU* 6.1 0.2 - - + -
149A TYR* 4.4 12.3 - - + +
151A PHE* 3.5 42.8 - - + -
174A TYR* 2.9 39.6 + - + +
175A TYR* 3.8 5.2 - - + +
176A SER 3.1 0.2 - - - -
177A THR* 1.3 75.8 + - - +
179A LEU* 1.3 65.4 + - - +
181A ALA* 3.5 2.7 + - - +
182A LEU* 3.2 49.9 + - + +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.6 35.7 - - + -
153A ILE* 5.8 0.9 - - + -
175A TYR* 3.0 23.7 + - + +
176A SER 4.1 2.0 - - - +
178A LEU* 1.3 75.0 - - - +
180A ASP* 1.3 63.9 + - - +
182A LEU* 4.1 4.5 - - + +
183A VAL* 3.2 28.2 + - - +
189A PRO* 3.7 15.3 - - + -
191A VAL* 5.2 1.1 - - + -
229A PHE* 3.7 34.5 - - + +
232A ARG* 4.3 19.8 - - + +
233A VAL* 3.7 33.4 - - + -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 2.9 27.9 + - - +
177A THR* 4.0 9.9 - - - +
179A LEU* 1.3 78.9 - - - +
181A ALA* 1.3 62.9 + - - +
183A VAL* 3.4 5.5 + - - +
184A LEU* 3.1 32.6 + - + +
232A ARG* 2.4 39.1 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 5.4 1.3 - - - +
138A LEU* 3.7 31.2 - - + -
177A THR 3.3 16.8 + - - +
178A LEU* 4.2 2.7 - - - +
180A ASP* 1.3 78.4 - - - +
182A LEU* 1.3 58.2 + - - +
184A LEU* 3.2 12.9 + - + +
185A ARG* 2.9 40.8 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.2 12.3 - - + -
141A LEU* 3.7 29.8 - - + -
149A TYR* 3.8 24.0 - - + +
151A PHE* 4.5 5.4 - - + -
178A LEU* 3.2 33.8 + - + +
179A LEU* 4.1 4.5 - - - +
180A ASP 3.3 0.2 - - - -
181A ALA* 1.3 77.5 - - - +
183A VAL* 1.3 56.1 + - - +
185A ARG* 3.3 3.4 + - - -
186A ASN 3.2 3.3 + - - -
187A ILE* 2.7 63.9 + - + +
189A PRO* 4.3 21.8 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU 3.2 19.1 + - - +
180A ASP* 3.9 4.5 - - - +
182A LEU* 1.3 73.9 - - - +
184A LEU* 1.3 64.4 + - + +
186A ASN* 3.1 13.0 + - - +
187A ILE 4.4 3.1 - - - +
188A GLU* 5.5 3.6 - - - +
189A PRO* 4.4 11.9 - - + -
232A ARG* 4.1 33.7 - - + +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.1 24.4 + - + +
181A ALA* 3.2 16.4 + - + +
183A VAL* 1.3 79.3 - - + +
185A ARG* 1.3 59.1 + - + +
186A ASN* 3.5 2.4 + - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 3.9 9.7 + - - -
138A LEU* 3.8 45.5 - - - +
139A SER* 5.4 1.2 + - - +
142A ASP* 2.4 45.7 + - - +
181A ALA* 2.9 24.2 + - - +
182A LEU 3.9 3.6 - - - +
183A VAL 3.2 0.4 - - - -
184A LEU* 1.3 78.9 - - + +
186A ASN* 1.3 70.1 + - - +
187A ILE* 3.2 25.0 + - + +
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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