Contacts of the helix formed by residues 114 - 130 (chain D) in PDB entry 3N3B
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 THR 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR* 6.5 0.7 - - + -
259A ASN* 4.9 13.5 - - + +
263A MET* 4.6 8.3 - - + -
269A PRO* 4.3 25.8 - - + -
20D ARG* 4.2 2.0 - - - -
110D GLU 4.8 0.2 + - - -
113D GLY* 1.3 77.1 - - - +
115D GLN* 1.3 63.9 + - - +
116D SER* 3.5 12.8 + - - -
117D ASP* 2.9 39.1 + - - +
118D ILE* 3.1 12.8 + - - +
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Residues in contact with GLN 115 (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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268A GLU* 4.0 13.9 - - - +
269A PRO* 5.2 4.7 - - + +
20D ARG* 3.9 11.1 + - - +
114D THR* 1.3 75.9 - - - +
116D SER* 1.3 56.3 + - - +
118D ILE* 3.4 29.3 + - - +
119D GLU* 3.0 48.4 + - - +
122D ARG* 5.5 3.2 - - - +
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Residues in contact with SER 116 (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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273A ALA* 3.4 28.9 + - - +
114D THR* 3.5 10.8 + - - -
115D GLN* 1.3 79.4 - - - +
117D ASP* 1.3 58.4 + - - +
119D GLU* 3.5 11.3 + - - +
120D ASN* 3.0 42.2 + - - +
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Residues in contact with ASP 117 (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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17D PHE* 4.5 5.4 - - + -
107D TYR* 2.7 31.3 + - + +
108D ARG 4.6 0.9 - - - +
109D PHE* 3.6 24.0 - - + +
110D GLU* 4.5 4.2 + - - +
113D GLY* 3.5 11.7 - - - -
114D THR* 2.9 39.4 + - - +
116D SER* 1.3 76.1 - - - +
118D ILE* 1.3 63.5 + - - +
120D ASN* 3.5 1.2 + - - +
121D VAL* 3.1 31.7 + - - +
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Residues in contact with ILE 118 (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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17D PHE* 4.2 21.3 - - + +
20D ARG* 3.5 60.8 - - + +
21D LEU* 4.0 11.7 - - + +
114D THR 3.1 10.0 + - - +
115D GLN* 3.6 27.4 - - - +
116D SER 3.4 0.2 - - - -
117D ASP* 1.3 75.9 - - - +
119D GLU* 1.3 59.9 + - - +
121D VAL* 3.5 3.9 + - - +
122D ARG* 3.1 57.5 + - - +
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Residues in contact with GLU 119 (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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115D GLN* 3.0 39.3 + - - +
116D SER* 3.8 10.0 + - - +
117D ASP 3.3 0.2 - - - -
118D ILE* 1.3 77.6 - - - +
120D ASN* 1.3 65.0 + - - +
122D ARG* 3.6 16.5 + - - +
123D LYS* 3.3 27.6 + - - +
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Residues in contact with ASN 120 (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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107D TYR* 3.2 39.5 + - + +
116D SER* 3.0 28.2 + - - +
117D ASP 4.0 0.4 - - - +
118D ILE 3.4 0.2 - - - -
119D GLU* 1.3 77.3 - - - +
121D VAL* 1.3 61.1 + - - +
123D LYS* 4.2 3.6 - - - +
124D GLY* 2.9 25.8 + - - -
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Residues in contact with VAL 121 (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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4D LEU* 5.4 2.0 - - + -
17D PHE* 3.8 19.7 - - + -
21D LEU* 4.0 26.9 - - + -
23D LEU* 5.3 1.8 - - + -
45D ILE* 5.7 0.9 - - + -
79D ILE* 4.5 19.3 - - + -
107D TYR* 4.1 24.5 - - + -
117D ASP 3.1 19.0 + - - +
118D ILE* 3.9 3.6 - - - +
120D ASN* 1.3 74.9 - - - +
122D ARG* 1.3 58.7 + - - +
124D GLY* 4.8 0.7 - - - -
125D VAL* 2.8 51.0 + - + +
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Residues in contact with ARG 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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20D ARG 3.6 14.1 + - - -
21D LEU* 2.8 40.9 + - + -
22D GLY* 5.0 0.6 - - - -
23D LEU* 5.0 12.2 - - + +
115D GLN* 5.5 4.2 - - - +
118D ILE* 3.1 39.1 + - - +
119D GLU* 3.8 15.3 - - - +
121D VAL* 1.3 79.1 - - - +
123D LYS* 1.3 58.4 + - - +
125D VAL* 4.4 2.5 - - - +
126D THR* 2.9 32.3 + - - +
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Residues in contact with LYS 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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119D GLU 3.3 15.6 + - - +
120D ASN* 4.2 4.7 - - - +
121D VAL 3.3 0.2 - - - -
122D ARG* 1.3 78.7 - - - +
124D GLY* 1.3 62.0 + - - +
126D THR* 3.4 8.8 + - - +
127D GLU* 3.3 43.9 - - + +
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Residues in contact with GLY 124 (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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106D LEU* 6.1 0.4 - - - +
120D ASN 2.9 20.4 + - - -
121D VAL* 3.6 0.7 - - - -
123D LYS* 1.3 77.2 - - - +
125D VAL* 1.3 63.1 + - - +
127D GLU* 4.1 5.3 - - - +
128D PHE* 3.2 24.1 + - - +
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Residues in contact with VAL 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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3D GLN 6.3 0.2 - - - -
4D LEU* 4.7 13.5 - - + -
23D LEU* 4.7 17.9 - - + -
43D ILE* 4.1 17.0 - - + -
79D ILE* 4.7 10.8 - - + -
106D LEU* 6.2 1.1 - - + -
121D VAL* 2.8 39.9 + - + +
122D ARG 4.4 2.0 - - - +
124D GLY* 1.3 70.4 - - - +
126D THR* 1.3 67.9 + - + +
128D PHE* 3.1 15.1 + - - +
129D TRP* 3.2 44.9 + - + +
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Residues in contact with THR 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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23D LEU* 6.0 7.4 - - + -
122D ARG 2.9 20.7 + - - +
123D LYS* 3.4 9.5 + - - +
125D VAL* 1.3 80.4 - - + +
127D GLU* 1.3 65.4 + - - +
128D PHE 3.6 0.2 + - - -
129D TRP* 3.8 6.2 + - - +
130D GLN* 3.4 38.5 + - - +
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Residues in contact with GLU 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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123D LYS* 3.3 35.2 + - + +
124D GLY* 4.2 4.8 - - - +
125D VAL 3.3 0.4 - - - -
126D THR* 1.3 77.2 + - - +
128D PHE* 1.3 64.4 + - - +
130D GLN* 3.7 15.9 + - - +
131D ARG* 3.6 33.2 + - - +
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Residues in contact with PHE 128 (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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43D ILE* 3.7 28.9 - - + -
76D ARG* 3.7 46.7 - - + -
104D PRO* 4.6 7.6 - - + -
106D LEU* 4.1 30.5 - - + -
124D GLY 3.2 18.8 + - - +
125D VAL* 3.1 8.4 + - - +
127D GLU* 1.3 77.2 - - - +
129D TRP* 1.3 73.6 + + - +
131D ARG* 3.1 35.2 + - - +
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Residues in contact with TRP 129 (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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3D GLN* 3.7 31.6 + - - +
41D PRO* 3.8 20.6 - - + -
42D TYR 3.7 27.1 - - - -
43D ILE* 3.7 25.4 - - + +
76D ARG* 4.2 17.3 - - + -
125D VAL* 3.2 44.6 + - + +
126D THR* 3.8 6.3 + - - +
128D PHE* 1.3 89.4 - + - +
130D GLN* 1.3 63.6 + - + +
131D ARG 3.2 5.3 + - - +
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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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126D THR* 3.4 29.2 + - - +
127D GLU* 4.1 10.5 - - - +
128D PHE 3.3 0.8 - - - -
129D TRP* 1.3 79.6 - - + +
131D ARG* 1.3 62.1 + - + +
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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