Contacts of the helix formed by residues 119 - 136 (chain D) 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 TYR 119 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 3.9 10.1 - - - +
86D SER 2.8 16.5 + - - +
87D THR* 3.5 22.4 - - + +
88D ARG 4.8 0.2 - - - +
89D GLY 4.8 0.2 + - - -
117D ASP* 3.6 34.8 - - + -
118D THR* 1.3 71.1 - - - +
120D MET* 1.3 63.2 + - - +
121D HIS* 3.2 32.8 - + + -
122D GLU* 3.1 28.8 + - + +
123D GLY 3.8 1.9 + - - -
157D LEU* 3.7 26.1 - - + +
160D TYR* 5.9 2.0 - + - -
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Residues in contact with MET 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ILE* 4.8 0.2 - - + -
85D PHE* 3.4 43.3 - - + -
118D THR 3.1 5.9 + - - -
119D TYR* 1.3 71.7 - - - +
121D HIS* 1.3 65.7 + - - +
123D GLY* 2.9 13.9 + - - -
124D PHE* 3.2 25.8 + - + -
147D ALA* 4.7 6.7 - - - -
149D THR* 3.9 26.7 - - + -
153D LEU* 3.9 20.6 - - + +
158D PHE* 5.5 0.2 - - + -
161D SER* 3.3 25.0 + - - +
188D LEU* 5.4 1.1 - - + -
191D ILE* 3.7 40.2 - - + -
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Residues in contact with HIS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D TYR* 3.5 40.1 - + + -
120D MET* 1.3 75.9 - - - +
122D GLU* 1.3 77.3 + - + +
124D PHE* 3.1 6.7 + - - +
125D GLU* 2.9 46.4 + - - +
157D LEU* 4.5 5.0 + - + +
160D TYR* 3.4 63.1 - + + +
161D SER* 3.2 13.1 + - - +
163D ARG* 6.1 1.3 - - - -
164D GLU* 3.7 11.3 - - + +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D THR 4.7 3.6 - - - +
88D ARG* 3.3 25.1 + - - +
89D GLY* 2.8 35.9 + - - +
119D TYR* 3.1 17.3 + - + +
120D MET 3.1 0.6 - - - -
121D HIS* 1.3 91.6 + - + +
123D GLY* 1.3 65.4 + - - +
125D GLU* 3.2 23.8 + - - +
126D ARG* 3.0 35.5 + - - +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 3.6 28.5 - - - +
83D ILE* 3.6 16.8 - - - +
85D PHE* 4.3 9.6 - - - +
89D GLY* 4.1 3.1 - - - -
119D TYR 3.8 2.0 + - - -
120D MET 2.9 10.5 + - - -
122D GLU* 1.3 79.0 - - - +
124D PHE* 1.3 59.3 + - - +
126D ARG* 3.4 6.1 + - - +
127D ALA* 3.3 15.6 + - - +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ILE* 3.8 16.8 - - + -
120D MET* 3.2 33.3 + - + -
121D HIS* 3.1 9.7 + - - +
123D GLY* 1.3 72.8 - - - +
125D GLU* 1.3 59.5 + - - +
127D ALA* 3.1 2.6 + - - +
128D SER* 2.8 33.7 + - - -
145D ILE* 3.9 14.8 - - + -
147D ALA* 4.0 15.9 - - + -
161D SER* 4.7 6.5 - - - -
164D GLU* 3.7 17.5 - - + +
165D ALA* 3.8 18.4 - - + -
168D SER* 3.6 17.2 + - - -
175D VAL* 3.7 25.1 - - + -
191D ILE* 3.5 32.3 - - + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D HIS* 2.9 26.7 + - - +
122D GLU* 3.4 33.1 - - - +
124D PHE* 1.3 77.2 - - - +
126D ARG* 1.3 72.9 + - - +
128D SER* 3.4 5.7 + - - -
129D GLU* 3.0 40.5 + - - +
164D GLU* 3.7 26.9 - - - +
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Residues in contact with ARG 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ILE* 3.7 14.8 - - + -
89D GLY 3.0 36.7 + - - +
90D THR* 3.8 4.0 - - - +
91D THR* 3.3 29.4 + - - +
122D GLU* 3.0 37.7 + - - +
123D GLY 3.6 7.2 - - - +
124D PHE 3.3 0.2 - - - -
125D GLU* 1.3 91.8 + - - +
127D ALA* 1.3 61.9 + - - +
129D GLU* 2.7 46.0 + - - +
130D GLN* 3.3 27.9 + - - +
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 4.2 11.4 - - + -
48D ILE* 3.9 20.9 - - + -
83D ILE* 3.6 18.8 - - + +
123D GLY 3.3 2.4 + - - -
124D PHE 3.1 8.4 + - - +
126D ARG* 1.3 75.9 - - - +
128D SER* 1.3 59.3 + - - +
130D GLN* 3.1 6.1 + - - +
131D ILE* 2.9 33.0 + - + +
145D ILE* 3.9 21.1 - - + -
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PHE 2.8 18.3 + - - -
125D GLU* 3.8 6.7 - - - -
127D ALA* 1.3 73.2 - - - +
129D GLU* 1.3 58.7 + - - +
131D ILE* 4.3 6.3 - - - +
132D TYR* 2.9 32.4 + - - +
164D GLU* 4.2 7.5 + - - -
167D ARG* 4.3 3.3 - - - +
168D SER* 2.8 37.8 + - - -
171D LEU* 3.6 19.4 - - - +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLU* 3.0 23.6 + - + +
126D ARG* 2.7 47.0 + - - +
128D SER* 1.3 75.5 - - - +
130D GLN* 1.3 62.9 + - + +
132D TYR* 3.7 7.5 + - - +
133D TYR* 3.3 21.3 + - - +
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Residues in contact with GLN 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 3.7 17.3 - - + +
81D SER* 2.9 23.2 + - - -
83D ILE* 3.8 10.3 - - - +
91D THR* 3.5 20.2 - - - +
94D LYS* 3.6 23.1 - - + +
95D LEU* 3.0 31.9 + - + +
126D ARG 3.3 17.4 + - - +
127D ALA 3.1 6.8 + - - +
129D GLU* 1.3 75.5 - - + +
131D ILE* 1.3 59.1 + - - +
133D TYR* 3.3 8.2 + - - +
134D GLU* 2.9 35.1 + - + +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 3.5 32.5 - - + +
127D ALA 2.9 27.4 + - - +
128D SER* 3.3 9.2 + - - +
130D GLN* 1.3 74.6 - - - +
132D TYR* 1.3 53.9 + - - +
134D GLU* 3.2 3.8 + - + +
135D ASN* 2.8 43.9 + - - +
143D SER* 4.3 14.4 - - - +
145D ILE* 4.1 13.5 - - + -
168D SER* 4.9 4.5 - - - +
171D LEU* 3.6 34.8 - - + +
173D ALA* 3.8 26.0 - - + +
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Residues in contact with TYR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASP* 4.0 16.5 + - - -
159B PHE* 3.5 49.0 - + - -
128D SER 2.9 17.9 + - - +
129D GLU* 3.8 7.9 - - - +
131D ILE* 1.3 78.4 - - - +
133D TYR* 1.3 66.0 + - + +
135D ASN* 3.4 18.0 + - + +
136D ARG* 3.4 46.6 + - + +
171D LEU* 4.2 12.3 - - + +
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU 3.3 10.8 + - - +
130D GLN* 3.3 10.8 + - - +
132D TYR* 1.3 82.9 - - + +
134D GLU* 1.3 94.0 + - + +
136D ARG* 3.2 21.2 + - + +
137D GLN* 3.3 38.6 + - - +
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Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASP* 4.1 9.0 - - - +
46D TYR* 3.8 4.7 - - - +
79D ARG* 2.8 33.7 + - - +
95D LEU* 3.6 29.6 - - + +
130D GLN* 2.9 21.4 + - + +
131D ILE* 3.7 6.3 - - + +
133D TYR* 1.3 97.1 - - - +
135D ASN* 1.3 68.5 + - - +
137D GLN* 3.0 32.8 + - - +
138D GLY 4.0 1.7 + - - -
139D TYR* 5.0 3.5 + - - +
141D THR* 5.8 7.2 - - + +
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Residues in contact with ASN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.5 32.7 - - + +
39A CYS* 3.2 18.2 - - - +
220A CYS* 3.4 1.0 - - - -
131D ILE* 2.8 28.3 + - - +
132D TYR* 3.4 9.9 - - + +
133D TYR 3.3 0.2 - - - -
134D GLU* 1.3 73.6 - - - +
136D ARG* 1.3 57.1 + - + +
137D GLN 3.0 0.2 - - - -
138D GLY* 2.9 20.3 + - - -
139D TYR 4.8 3.6 + - - +
141D THR* 4.9 8.0 + - - -
171D LEU* 3.0 45.7 + - - +
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 3.8 12.3 - - - -
220A CYS* 3.4 18.0 - - + +
132D TYR* 3.4 46.3 + - + +
133D TYR* 3.2 16.4 + - + +
134D GLU 3.2 1.0 - - - -
135D ASN* 1.3 75.5 - - + +
137D GLN* 1.3 66.2 + - - +
138D GLY 3.3 0.2 - - - -
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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
------------------------------------------------------------
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