Contacts of the helix formed by residues 158 - 173 (chain A) in PDB entry 3NNJ
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 GLY 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL* 4.0 6.7 - - - +
156A PHE* 3.4 20.6 + - - -
157A PRO* 1.3 70.9 - - - +
159A GLN* 1.3 66.0 + - - +
160A PHE 3.1 0.4 - - - -
161A TYR* 2.9 22.9 + - - +
162A TYR* 3.6 8.9 - - - -
225A TYR* 3.2 29.9 + - - +
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Residues in contact with GLN 159 (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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126A THR* 3.8 23.6 - - + +
127A GLU* 4.4 14.7 - - - +
157A PRO* 3.2 4.8 + - + -
158A GLY* 1.3 76.8 - - - +
160A PHE* 1.3 62.8 + - - +
162A TYR* 3.1 20.6 + - - +
163A SER* 4.2 1.7 + - - -
225A TYR* 3.4 46.8 + - + +
159B GLN* 5.9 2.8 - - - +
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Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.6 25.4 - + - -
157A PRO* 3.1 27.9 + - + +
158A GLY 3.0 1.0 + - - -
159A GLN* 1.3 77.2 - - - +
161A TYR* 1.3 76.6 + + + +
163A SER* 3.2 12.3 + - - +
164A VAL* 3.6 15.3 + - + +
196A ILE* 4.3 18.6 - - + -
160B PHE* 3.8 23.8 - + + +
163B SER* 3.7 33.4 + - - +
164B VAL* 3.9 22.4 - - + -
167B LEU* 3.9 18.8 - - + -
192B ILE* 3.7 23.8 - - + -
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Residues in contact with TYR 161 (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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114A TRP 5.6 4.1 + - - -
115A HIS* 5.9 4.0 - - - -
116A VAL* 4.0 19.1 - - + -
118A VAL* 4.2 11.0 - - + -
156A PHE* 3.9 21.1 - + - -
158A GLY* 2.9 16.2 + - - +
160A PHE* 1.3 91.7 - + + +
162A TYR* 1.3 64.2 + - - +
164A VAL* 3.3 10.4 + - + -
165A PHE* 3.0 21.6 + - + +
193A TYR* 3.7 37.2 + + - -
196A ILE* 3.8 43.0 + - + +
201A ILE* 4.3 13.5 - - + +
227A LEU* 5.5 3.6 - - + -
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.5 14.2 + - + -
117A GLY 3.4 10.4 + - - -
118A VAL* 3.5 38.1 - - + -
121A PHE* 5.1 5.2 - - + -
126A THR* 3.6 35.9 - - + +
158A GLY 3.6 9.0 - - - -
159A GLN* 3.1 19.6 + - - +
161A TYR* 1.3 76.8 - - - +
163A SER* 1.3 56.7 + - - +
165A PHE* 3.3 3.1 + - - +
166A ASP* 2.9 33.4 + - - +
224A LYS* 2.6 59.7 + - + +
225A TYR* 3.9 10.1 - + - -
259A ARG* 4.6 9.2 - - - +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 5.7 2.3 + - - +
159A GLN 4.2 1.1 + - - -
160A PHE* 3.2 11.2 + - - -
162A TYR* 1.3 76.4 - - - +
164A VAL* 1.3 62.3 + - - +
166A ASP* 3.8 9.0 + - - +
167A LEU* 2.9 35.0 + - - +
157B PRO* 4.8 18.8 + - - +
160B PHE* 4.1 25.0 - - - +
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Residues in contact with VAL 164 (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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160A PHE* 3.6 27.1 + - + +
161A TYR* 3.3 12.0 + - + +
163A SER* 1.3 77.3 - - - +
165A PHE* 1.3 60.8 + - - +
167A LEU* 3.1 10.9 + - - +
168A HIS* 3.0 22.4 + - - +
192A ILE* 3.9 17.7 - - + +
193A TYR* 3.3 42.9 + - + +
196A ILE* 4.4 8.7 - - + -
160B PHE* 3.9 25.6 - - + -
164B VAL* 5.8 0.4 - - + -
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Residues in contact with PHE 165 (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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118A VAL* 3.3 48.0 - - + -
119A GLY* 4.7 7.0 - - - -
161A TYR* 3.0 12.3 + - + +
162A TYR* 3.4 9.9 - + - +
164A VAL* 1.3 74.4 - - - +
166A ASP* 1.3 74.5 + - - +
168A HIS* 3.1 8.1 + + - +
169A LEU* 2.9 32.9 + - + +
193A TYR* 4.1 31.6 - + + -
259A ARG* 4.4 9.4 - - - -
263A PHE* 4.3 28.7 - + - -
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 4.4 2.8 + - - -
162A TYR 2.9 20.5 + - - +
163A SER* 3.8 9.7 + - - +
164A VAL 3.3 0.2 - - - -
165A PHE* 1.3 86.1 - - - +
167A LEU* 1.3 60.5 + - - +
169A LEU* 3.3 7.2 + - - +
170A LYS* 3.0 30.6 + - + +
256A ASP* 4.8 1.2 - - - +
259A ARG* 2.9 47.8 + - - +
262A LEU* 4.5 6.5 - - + +
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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
----------------------------------------------------------
163A SER 2.9 21.6 + - - +
164A VAL* 3.1 9.6 + - - +
166A ASP* 1.3 76.1 - - - +
168A HIS* 1.3 62.9 + - - +
170A LYS* 3.3 13.3 + - + +
171A ASN* 3.0 22.7 + - - +
174A LYS* 5.2 0.7 + - - -
191A THR* 5.4 1.7 - - - +
192A ILE* 4.4 15.5 - - + -
155B ILE* 3.3 26.9 - - + +
156B PHE* 4.6 8.7 - - + -
157B PRO* 4.4 11.4 - - + -
160B PHE* 4.0 31.0 - - + -
204B THR* 4.3 20.4 - - + -
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL 3.0 5.1 + - - +
165A PHE* 3.1 11.6 + + - +
167A LEU* 1.3 75.7 - - - +
169A LEU* 1.3 65.3 + - - +
171A ASN* 3.1 7.1 + - - +
172A ASN* 2.9 50.5 + - - +
186A VAL* 3.7 25.7 - - - +
189A ALA* 5.0 1.3 - - + -
191A THR* 2.8 36.0 + - + +
193A TYR* 3.4 44.4 - + + +
194A ASN* 3.6 17.7 + - - -
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Residues in contact with LEU 169 (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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165A PHE* 2.9 24.1 + - + +
166A ASP* 3.3 6.7 + - - +
168A HIS* 1.3 77.3 - - - +
170A LYS* 1.3 61.2 + - - +
172A ASN* 3.1 27.7 + - - +
173A ILE* 3.4 8.0 + - + +
259A ARG* 4.0 16.2 - - + -
262A LEU* 3.4 48.7 - - + +
263A PHE* 3.9 32.8 - - + -
266A TYR* 4.1 21.5 - - + -
280A TYR* 5.5 0.7 - - + -
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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
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166A ASP* 3.0 20.2 + - + +
167A LEU* 3.5 19.5 - - + +
168A HIS 3.1 0.2 - - - -
169A LEU* 1.3 74.3 - - - +
171A ASN* 1.3 63.5 + - - +
173A ILE* 3.3 24.3 + - + +
174A LYS* 3.5 21.8 + - - +
262A LEU* 3.7 32.5 - - + +
154B LYS 4.0 21.6 + - - +
155B ILE* 5.2 7.0 - - - +
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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
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167A LEU 3.0 13.6 + - - +
168A HIS 3.5 7.4 - - - +
170A LYS* 1.3 75.0 - - - +
172A ASN* 1.3 66.6 + - - +
174A LYS* 3.2 22.9 + - - +
185A TYR* 3.0 34.0 + - - -
189A ALA* 3.4 18.0 - - - +
191A THR* 3.6 17.7 - - + +
203B TYR* 3.0 23.4 + - - +
204B THR* 5.7 0.9 - - - +
206B LYS* 2.9 30.3 + - - -
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Residues in contact with ASN 172 (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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168A HIS* 2.9 45.2 + - - +
169A LEU* 3.1 22.5 - - - +
171A ASN* 1.3 82.7 + - - +
173A ILE* 1.3 55.7 + - - +
175A TRP* 3.3 24.8 - - - +
182A LEU* 4.7 0.3 - - - +
185A TYR* 4.0 5.8 - - - -
186A VAL* 3.3 30.2 - - - +
266A TYR* 3.4 36.6 + - + -
269A LEU* 4.2 0.7 - - - +
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Residues in contact with ILE 173 (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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169A LEU* 3.8 9.9 - - + +
170A LYS* 3.3 19.3 + - + +
172A ASN* 1.3 74.0 - - - +
174A LYS* 1.3 59.8 + - + +
175A TRP 3.0 9.3 + - - +
262A LEU* 3.7 32.3 - - + +
265A LYS* 4.1 22.4 - - + +
266A TYR* 3.4 41.3 - - + +
269A LEU* 3.8 18.5 - - + +
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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