Contacts of the helix formed by residues 165 - 182 (chain A) in PDB entry 4NKU
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.4 2.8 - - + -
105A CYS* 3.0 21.8 - - + -
162A GLY* 5.4 2.2 - - - -
163A PHE 3.1 8.3 + - - +
164A ASN* 1.3 74.6 - - - +
166A ARG* 1.3 59.4 + - - +
167A LEU* 3.8 9.5 - - - +
168A ALA* 3.3 28.1 + - + +
169A ILE* 3.4 14.6 + - - +
58D A 2.9 38.9 + - - +
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 5.7 1.0 + - - -
107A LEU* 4.0 35.2 - - + +
108A MET 3.0 24.7 + - - -
109A ASP 4.9 3.0 - - - -
164A ASN* 3.2 30.7 + - - +
165A ASN* 1.3 75.1 - - - +
167A LEU* 1.3 62.7 + - - +
169A ILE* 3.2 10.8 + - + +
170A HIS* 3.0 34.2 + - + +
245A VAL* 3.8 26.5 - - + -
246A ASP* 3.9 13.7 + - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 3.2 8.7 - - - +
166A ARG* 1.3 75.9 - - - +
168A ALA* 1.3 59.1 + - - +
170A HIS* 3.2 4.3 + - - +
171A ASN* 3.0 32.7 + - - +
245A VAL* 3.7 25.6 - - + +
246A ASP* 3.8 22.2 + - + +
248A PHE* 3.7 32.5 - - + -
250A VAL* 3.9 21.8 - - + -
332A PHE* 4.8 5.5 - - + +
333A GLU* 4.2 29.8 - - + +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.6 27.4 - - + -
165A ASN* 3.3 33.8 - - - +
167A LEU* 1.3 78.0 - - - +
169A ILE* 1.3 63.1 + - - +
171A ASN* 3.0 22.0 - - - +
172A THR* 3.0 20.8 + - - -
58D A 4.0 7.2 - - - +
59D U 3.4 6.0 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.8 30.3 - - + -
87A ALA 5.6 0.7 - - - +
88A PHE* 4.2 21.1 - - + -
105A CYS* 4.2 5.4 - - + -
107A LEU* 3.6 42.0 - - + -
165A ASN 3.4 11.4 + - - +
166A ARG* 3.2 11.4 + - + +
167A LEU 3.2 0.4 - - - -
168A ALA* 1.3 79.2 - - - +
170A HIS* 1.3 64.8 + - + +
172A THR* 3.3 5.5 + - - -
173A LEU* 3.0 35.4 + - + +
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Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 3.0 35.8 + - + +
167A LEU 3.2 6.0 + - - +
169A ILE* 1.3 80.3 - - + +
171A ASN* 1.3 64.8 + - - +
173A LEU* 3.2 25.4 + - + +
174A LEU 3.0 18.4 + - - -
243A LYS* 4.5 16.5 + - + -
245A VAL* 3.9 23.5 - - + +
250A VAL* 3.6 46.1 + - + +
252A PHE* 4.8 2.5 - - + -
332A PHE* 3.3 12.6 - - + -
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.0 22.9 + - - +
168A ALA* 3.0 5.8 - - - +
170A HIS* 1.3 76.7 - - - +
172A THR* 1.3 58.5 + - - +
174A LEU* 3.4 2.4 + - + +
175A LEU* 3.0 34.8 + - + +
212A TYR* 3.3 30.8 + - + +
330A ASP* 3.9 9.8 + - - +
331A PRO* 5.0 3.8 - - + -
332A PHE* 3.8 18.1 - - + -
59D U 2.5 53.2 + - - +
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 5.2 0.2 - - - +
88A PHE* 3.4 5.9 - - - +
89A GLY* 2.8 43.8 + - - +
92A GLU* 3.8 23.8 - - + -
93A SER* 4.2 7.6 - - - +
168A ALA 3.0 13.6 + - - -
169A ILE 3.5 9.0 - - - -
171A ASN* 1.3 76.8 + - - +
173A LEU* 1.3 55.1 + - - +
175A LEU* 3.3 6.8 + - - +
176A SER* 2.8 35.0 + - - -
59D U 3.2 8.9 + - - -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.0 23.9 + - + +
170A HIS* 3.4 35.2 - - + +
172A THR* 1.3 76.1 - - - +
174A LEU* 1.3 62.3 + - - +
176A SER* 3.4 8.8 + - - -
177A SER* 3.1 26.5 + - - -
243A LYS* 6.1 1.8 - - - +
252A PHE* 3.9 14.5 - - + -
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Residues in contact with LEU 174 (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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170A HIS 3.0 12.7 + - - +
171A ASN* 3.6 7.6 - - - +
172A THR 3.3 0.2 - - - -
173A LEU* 1.3 76.3 - - - +
175A LEU* 1.3 70.3 + - + +
177A SER* 3.2 11.8 + - - -
178A TYR* 3.2 43.8 + - + -
216A LEU* 6.1 0.2 - - + -
219A LEU* 5.7 2.2 - - + -
234A LEU* 4.4 2.5 - - + -
235A LEU* 3.8 31.2 - - + -
252A PHE* 3.9 32.9 - - + -
292A PHE* 6.2 1.3 - - + -
331A PRO* 3.9 24.0 - - + -
332A PHE* 3.9 16.8 - - + -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 4.3 11.9 - - - +
95A LEU* 4.5 7.2 - - + -
171A ASN* 3.0 21.4 + - + +
172A THR* 3.8 5.2 - - - +
174A LEU* 1.3 85.7 - - + +
176A SER* 1.3 63.0 + - - +
178A TYR* 3.3 7.8 + - - +
179A THR* 3.0 28.3 + - - +
185A LEU* 4.8 0.3 - - - +
212A TYR* 3.9 32.5 - - + +
215A VAL* 3.6 28.3 - - + -
216A LEU* 4.5 6.7 - - + -
219A LEU* 3.8 23.8 - - + -
59D U 4.5 4.7 - - - +
101D BR 4.3 12.8 - - + -
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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
----------------------------------------------------------
92A GLU* 4.3 10.4 + - - -
93A SER* 4.1 16.2 + - - +
172A THR* 2.8 23.0 + - - -
173A LEU* 3.5 12.8 - - - -
175A LEU* 1.3 73.4 - - - +
177A SER* 1.3 61.6 + - - +
179A THR* 2.7 23.6 + - - -
180A LYS* 3.1 32.8 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 3.1 15.0 + - - -
174A LEU 3.2 8.7 + - - -
176A SER* 1.3 73.3 - - - +
178A TYR* 1.3 61.4 + - - +
180A LYS* 3.2 5.8 + - - +
181A LEU* 2.9 31.6 + - - +
234A LEU* 4.2 5.8 - - - -
252A PHE* 3.5 25.2 - - - -
254A ASP* 4.9 2.6 - - - +
256A LEU* 3.9 31.5 - - - +
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Residues in contact with TYR 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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174A LEU* 3.2 47.6 + - + +
175A LEU* 3.7 6.5 - - - +
177A SER* 1.3 80.7 - - - +
179A THR* 1.3 61.1 + - - +
181A LEU* 3.1 18.8 + - + +
182A ASP 3.3 10.6 + - - +
185A LEU* 3.6 17.0 - - + +
219A LEU* 3.8 19.7 - - + -
223A ILE* 3.5 16.2 - - + +
231A PHE* 3.5 44.0 - + + -
232A PRO 3.0 19.3 + - - -
233A ASN* 3.5 5.4 + - - -
234A LEU* 2.9 42.2 + - + -
235A LEU* 5.0 1.9 - - + +
292A PHE* 6.4 0.4 - + - -
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Residues in contact with THR 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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93A SER 3.2 19.3 + - - +
94A GLY 5.9 0.4 - - - -
95A LEU* 3.6 40.6 - - + -
175A LEU 3.0 15.2 + - - +
176A SER* 2.7 18.5 + - - -
178A TYR* 1.3 76.7 - - - +
180A LYS* 1.3 62.9 + - - +
182A ASP 3.5 14.6 - - - +
183A ALA* 5.0 2.4 - - - -
185A LEU* 3.8 17.0 - - + -
186A LYS* 5.3 8.8 + - - +
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Residues in contact with LYS 180 (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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176A SER* 3.1 29.1 + - - +
177A SER* 3.2 8.3 + - - +
179A THR* 1.3 83.6 + - - +
181A LEU* 1.3 60.1 + - - +
182A ASP 3.5 0.4 + - - -
256A LEU* 4.1 21.7 - - + +
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Residues in contact with LEU 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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177A SER 2.9 12.2 + - - +
178A TYR* 3.1 30.7 + - + +
180A LYS* 1.3 80.8 - - - +
182A ASP* 1.3 61.2 + - - +
231A PHE* 3.7 15.3 - - + -
232A PRO* 4.4 5.4 - - + -
234A LEU* 4.3 24.7 - - + -
256A LEU* 4.4 17.3 - - + +
259A ILE* 3.8 39.9 - - + +
260A PRO 5.5 1.1 - - - +
261A PRO* 6.0 1.6 - - - +
262A SER 5.9 1.0 + - - -
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Residues in contact with ASP 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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178A TYR 3.3 3.0 + - - -
179A THR 3.5 12.9 - - - +
180A LYS 3.5 1.3 - - - -
181A LEU* 1.3 82.0 - - - +
183A ALA* 1.3 66.8 + - - +
184A ARG* 2.9 66.7 + - - +
185A LEU* 3.2 15.7 + - - +
186A LYS 4.5 0.9 + - - -
230A VAL* 3.9 6.8 - - - +
231A PHE* 3.3 25.1 - - + -
262A SER* 3.7 16.3 + - - -
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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