Contacts of the helix formed by residues 154 - 171 (chain A) in PDB entry 3N2N
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 HIS 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 6.2 0.9 - - + -
152A GLU 4.2 6.7 + - - -
153A LEU* 1.3 74.7 - - - +
155A GLU* 1.3 68.1 + - - +
156A ASP 3.4 2.7 - - - +
157A LEU* 3.0 30.0 + - + +
158A PHE* 2.9 19.4 + - - +
221A ACT 5.0 12.2 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU 3.8 0.8 + - - -
154A HIS* 1.3 72.6 - - - +
156A ASP* 1.3 70.1 + - - +
158A PHE* 3.2 7.0 + - - +
159A PHE* 3.1 20.8 + - - +
217C LYS 4.4 18.5 - - - +
219C SER 4.3 13.2 - - - +
220C CYS* 5.9 0.3 - - - -
136F ARG* 5.3 6.4 + - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 3.4 1.8 - - + +
155A GLU* 1.3 83.1 - - - +
157A LEU* 1.3 60.3 + - + +
159A PHE* 3.2 10.0 + - - +
160A TYR* 2.9 49.8 + - + +
132F TYR* 4.1 15.2 + - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 5.3 1.6 - - + -
118A THR* 3.4 36.1 - - - +
119A TYR* 3.8 48.0 - - + +
120A MET 5.6 0.6 + - - +
121A HIS* 4.7 4.3 + - + +
153A LEU* 4.0 5.8 - - + -
154A HIS* 3.0 41.3 + - + +
156A ASP* 1.3 78.3 - - + +
158A PHE* 1.3 59.2 + - - +
160A TYR* 3.4 16.2 + - + +
161A SER* 2.9 31.7 + - - -
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Residues in contact with PHE 158 (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 GLY* 3.4 23.1 - - - -
153A LEU* 3.5 36.9 - - + +
154A HIS 2.9 9.6 + - - +
155A GLU* 3.5 11.0 - - - +
157A LEU* 1.3 73.4 - - - +
159A PHE* 1.3 61.2 + - - +
161A SER* 3.3 0.5 + - - -
162A GLU* 2.9 31.1 + - + +
187A GLN* 3.4 66.4 - - + -
188A LEU* 4.4 6.3 - - + -
190A ARG* 4.7 8.1 - - + -
191A ILE* 3.7 25.8 - - + -
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 3.1 12.1 + - - +
156A ASP* 3.2 14.1 + - - +
158A PHE* 1.3 76.3 - - - +
160A TYR* 1.3 79.2 + + - +
162A GLU* 3.3 3.3 + - - -
163A ARG* 3.0 50.3 + - + +
37C MET* 3.4 44.9 - - + +
132F TYR* 3.6 42.8 - + - -
167F ARG* 5.7 1.8 - - - -
171F LEU* 4.0 19.3 - - + -
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Residues in contact with TYR 160 (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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119A TYR* 6.4 0.7 - + - -
121A HIS* 3.4 45.8 - + + +
156A ASP* 2.9 40.0 + - + +
157A LEU* 3.8 11.9 - - + +
158A PHE 3.4 0.2 - - - -
159A PHE* 1.3 86.0 - + - +
161A SER* 1.3 56.0 + - - +
163A ARG* 3.4 42.8 + - - +
164A GLU* 3.0 26.7 + - + +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 3.3 10.8 + - - +
121A HIS* 3.3 27.4 + - - +
124A PHE* 4.7 3.3 - - - -
153A LEU* 3.2 21.2 - - - +
157A LEU 2.9 19.7 + - - -
158A PHE 3.6 4.5 - - - -
159A PHE 3.2 0.2 - - - -
160A TYR* 1.3 74.0 - - - +
162A GLU* 1.3 60.0 + - - +
164A GLU* 3.8 1.0 - - - +
165A ALA* 2.9 31.9 + - - +
191A ILE* 3.7 15.7 - - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 2.9 19.0 + - - +
159A PHE* 5.5 0.7 - - - -
161A SER* 1.3 75.0 - - - +
163A ARG* 1.3 57.0 + - - +
165A ALA* 3.4 2.9 + - - +
166A ASN* 2.9 44.5 + - - +
190A ARG* 3.4 52.4 + - - +
191A ILE* 3.6 10.9 - - + +
36C SER 5.6 0.5 - - - -
37C MET* 3.4 44.3 - - + +
218C LYS* 5.8 1.7 + - - -
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.0 35.9 + - + +
160A TYR* 3.4 39.5 - - - +
161A SER 3.3 0.2 - - - -
162A GLU* 1.3 77.7 - - - +
164A GLU* 1.3 77.4 + - - +
166A ASN* 3.4 6.5 + - - +
167A ARG* 3.0 25.6 + - + +
37C MET* 3.9 13.6 - - + +
167F ARG* 3.5 49.2 - - + +
170F ASP* 5.8 1.6 - - - +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A HIS* 3.6 32.7 - - + +
124A PHE* 3.8 11.6 - - + +
125A GLU* 3.3 34.0 - - + +
128A SER* 4.2 4.0 + - - -
160A TYR* 3.0 20.1 + - + +
161A SER 4.1 2.0 - - - +
163A ARG* 1.3 94.6 + - - +
165A ALA* 1.3 60.8 + - - +
167A ARG* 3.3 20.7 + - - +
168A SER* 2.9 29.3 + - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.7 27.5 - - + -
161A SER 2.9 19.9 + - - +
162A GLU 3.8 2.7 - - - +
164A GLU* 1.3 75.1 - - - +
166A ASN* 1.3 59.1 + - - +
168A SER* 3.2 5.2 + - - -
169A ARG* 3.0 37.9 + - - +
175A VAL* 4.4 0.9 - - + +
191A ILE* 3.5 31.6 - - + +
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Residues in contact with ASN 166 (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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162A GLU* 2.9 27.1 + - - +
163A ARG* 3.5 6.0 - - - +
165A ALA* 1.3 76.4 - - - +
167A ARG* 1.3 56.4 + - - +
169A ARG* 2.8 40.2 + - - +
170A ASP* 2.9 34.1 + - - +
190A ARG 4.8 0.2 - - - +
37C MET* 3.8 18.8 - - - +
170F ASP* 3.4 35.2 + - - +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 4.1 14.4 - - - +
163A ARG* 3.0 14.5 + - + +
164A GLU* 3.4 23.3 - - - +
165A ALA 3.2 0.2 - - - -
166A ASN* 1.3 74.3 - - - +
168A SER* 1.3 64.0 + - - +
170A ASP* 3.3 15.2 + - - +
171A LEU* 3.1 49.2 + - + +
37D MET* 3.2 31.8 - - - +
159F PHE* 3.3 28.0 - - - -
163F ARG* 3.4 38.7 - - - +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.6 16.1 + - - -
128A SER* 2.8 23.6 + - - -
131A ILE* 4.9 2.6 - - - +
145A ILE* 3.8 24.8 - - - +
164A GLU 2.9 14.9 + - - -
165A ALA* 3.2 11.6 + - - -
167A ARG* 1.3 76.5 - - - +
169A ARG* 1.3 60.5 + - - +
171A LEU* 3.2 14.4 + - - +
172A GLY 3.2 0.7 + - - -
173A ALA* 3.0 26.5 + - - +
175A VAL* 4.6 2.5 - - - -
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Residues in contact with ARG 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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162A GLU 4.4 0.2 + - - -
165A ALA* 3.0 15.1 + - - +
166A ASN* 2.8 45.1 + - - +
168A SER* 1.3 76.5 - - - +
170A ASP* 1.3 62.0 + - - +
172A GLY* 2.9 20.3 + - - -
173A ALA 3.5 21.3 + - - +
175A VAL* 3.6 11.0 - - + +
190A ARG 3.8 10.9 + - - -
191A ILE 2.8 29.1 + - - -
192A ALA 3.4 11.9 + - - -
193A ASP* 3.1 36.1 + - - +
36D SER* 5.2 2.6 + - - -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 2.9 19.2 + - - +
167A ARG* 3.3 28.1 + - - +
169A ARG* 1.3 76.8 - - - +
171A LEU* 1.3 55.1 + - - +
172A GLY 3.2 1.0 + - - -
36D SER* 3.7 4.0 - - - +
37D MET* 2.8 40.2 + - + +
163F ARG* 5.4 1.4 - - - +
166F ASN* 3.2 35.7 + - - +
170F ASP* 5.3 3.1 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 3.7 44.2 - - - +
131A ILE* 3.7 17.5 - - + +
132A TYR* 4.1 16.4 - - + +
135A ASN* 3.0 35.8 + - - +
167A ARG* 3.1 43.9 + - + +
168A SER* 3.5 8.1 - - - +
169A ARG 3.1 0.4 - - - -
170A ASP* 1.3 76.1 - - - +
172A GLY* 1.3 57.3 + - - +
173A ALA 3.7 0.2 - - - -
36D SER* 3.8 6.4 + - - -
37D MET* 4.9 3.8 - - + +
38D ALA* 4.1 2.3 - - - +
159F PHE* 3.9 18.4 - - + -
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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
------------------------------------------------------------
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