Contacts of the helix formed by residues 119 - 131 (chain D) in PDB entry 3NDM
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 ALA 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D ASP* 3.8 6.9 - - + +
118D SER* 1.3 79.9 - - - +
120D PHE* 1.3 63.5 + - - +
121D PHE* 3.3 4.0 + - - -
122D TRP* 3.5 27.9 + - + +
123D GLU* 2.8 20.1 - - - +
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Residues in contact with PHE 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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87D PHE* 4.2 28.7 - + + -
105D LYS* 5.6 2.0 - - - -
107D LEU* 4.6 13.5 - - + -
112D MET* 3.6 42.8 - - + -
117D ASP* 4.0 28.9 + - - +
118D SER* 4.3 1.1 - - - -
119D ALA* 1.3 87.0 - - - +
121D PHE* 1.3 77.6 + + + +
123D GLU* 3.0 29.2 + - - +
124D GLU* 3.5 12.4 + - - +
218D GLY* 4.1 36.8 - - - +
219D THR* 5.6 0.7 - - - -
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Residues in contact with PHE 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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107D LEU* 4.5 12.8 - - + -
112D MET* 4.0 21.5 - - - -
118D SER 3.5 26.9 - - - -
120D PHE* 1.3 95.1 - + + +
122D TRP* 1.3 118.1 + + - +
124D GLU* 2.9 12.3 + - + +
125D ARG* 2.9 26.0 + - - +
149D LEU* 3.9 7.4 - - + -
151D MET* 4.9 1.5 - - - +
393D PRO 4.4 0.9 - - - -
394D PHE* 3.5 36.3 - + - -
397D PHE* 3.6 30.7 - + + -
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Residues in contact with TRP 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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58C ARG* 3.4 34.9 - - - +
118D SER 4.5 2.0 + - - -
119D ALA* 3.5 28.5 - - + +
120D PHE 3.2 0.2 - - - -
121D PHE* 1.3 108.2 - + - +
123D GLU* 1.3 66.6 + - - +
125D ARG* 3.8 23.0 + - - +
126D ASP* 3.1 30.4 + - - +
393D PRO 3.2 26.1 + - - -
394D PHE* 4.2 4.3 - - - -
395D VAL 4.0 0.7 - - - -
396D GLY* 3.6 11.2 - - - -
397D PHE* 3.3 43.3 - + + -
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Residues in contact with GLU 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 ALA* 2.8 26.0 - - - +
120D PHE* 3.0 20.4 - - - +
122D TRP* 1.3 76.7 - - - +
124D GLU* 1.3 64.7 + - - +
126D ASP* 3.8 4.7 - - - +
127D ILE* 2.9 27.9 + - - +
194D PHE* 3.7 24.9 - - + -
217D PHE 4.7 5.2 - - - +
219D THR 5.1 1.3 - - - -
220D CYS* 3.5 26.0 - - + +
221D MET* 5.5 1.8 - - - -
222D LYS 5.9 0.5 + - - -
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Residues in contact with GLU 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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105D LYS* 3.3 31.7 + - - +
107D LEU* 5.4 0.7 - - - +
120D PHE* 3.5 9.2 + - - +
121D PHE* 2.9 23.7 + - - +
123D GLU* 1.3 76.6 - - - +
125D ARG* 1.3 66.9 + - - +
127D ILE* 2.8 16.6 + - - +
128D MET* 3.0 21.8 + - - +
151D MET* 3.6 21.3 - - + +
153D MET* 5.7 0.7 - - - +
215D ALA 3.7 18.5 - - - +
216D ASP* 3.8 3.1 - - - +
217D PHE* 3.8 36.0 + - + -
218D GLY* 4.3 7.1 + - - -
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Residues in contact with ARG 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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21D PRO 5.0 7.3 + - - -
26D ASN* 5.4 1.4 - - - +
29D CYS* 4.8 6.1 - - - -
121D PHE 2.9 12.7 + - - +
122D TRP* 3.8 22.3 - - - +
124D GLU* 1.3 76.2 - - - +
126D ASP* 1.3 78.5 + - - +
127D ILE 3.1 1.0 + - - -
128D MET* 4.0 1.1 - - - -
129D ALA* 2.9 29.4 + - + +
130D PHE* 5.5 7.0 - - + -
139D LEU* 4.2 14.4 - - + -
142D ALA* 4.7 2.7 - - - -
151D MET* 3.8 18.1 - - + +
396D GLY 3.2 14.9 + - - -
397D PHE* 2.4 52.1 + - + -
398D THR 3.5 10.1 + - - -
399D TYR* 3.5 23.9 - - + +
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Residues in contact with ASP 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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22D LYS* 6.2 0.2 - - - +
122D TRP* 3.1 21.3 + - - +
123D GLU* 3.8 8.3 - - - +
125D ARG* 1.3 86.4 + - - +
127D ILE* 1.3 61.7 + - + +
130D PHE* 2.7 53.3 + - - +
194D PHE* 4.7 12.2 - - + -
222D LYS* 5.0 8.0 + - - -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D GLU 2.9 19.1 - - - +
124D GLU* 2.8 12.6 + - - +
126D ASP* 1.3 71.8 - - - +
128D MET* 1.3 58.9 + - - +
129D ALA 2.8 9.3 + - - -
130D PHE* 5.2 0.2 - - - -
131D ALA* 2.7 43.6 + - + +
136D VAL* 4.1 17.0 - - + -
189D ILE* 4.3 15.9 - - + -
192D MET* 4.5 16.8 - - + -
194D PHE* 3.4 39.9 - - + -
217D PHE* 4.3 25.1 - - + -
220D CYS* 4.3 6.1 - - - -
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Residues in contact with MET 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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124D GLU* 3.0 27.1 + - - +
125D ARG* 4.1 2.7 - - - +
127D ILE* 1.3 80.3 - - - +
129D ALA* 1.3 54.5 + - - +
131D ALA* 4.6 2.4 + - - +
132D ASN 5.6 0.7 + - - -
136D VAL* 4.3 0.4 - - - -
137D VAL* 3.2 47.6 - - + +
138D GLN* 3.3 4.2 - - - +
139D LEU* 2.6 37.1 + - + -
151D MET* 4.5 7.6 - - - -
153D MET* 3.1 40.6 - - - +
215D ALA 3.4 23.8 - - - +
217D PHE* 3.5 21.5 - - + -
900D 3ND 4.2 1.8 - - + -
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Residues in contact with ALA 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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125D ARG* 2.9 21.7 + - + +
126D ASP 3.7 2.9 - - - +
127D ILE 2.9 0.2 - - - -
128D MET* 1.3 79.9 - - - +
130D PHE* 1.3 74.7 + - + +
131D ALA 3.6 0.7 - - - -
132D ASN* 4.9 2.6 + - - +
138D GLN* 5.6 2.9 - - - +
139D LEU* 3.7 25.0 - - + +
399D TYR* 3.9 28.8 + - + -
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Residues in contact with PHE 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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21D PRO* 4.1 25.4 - - + -
22D LYS* 4.2 42.6 - - + +
125D ARG* 5.3 8.3 - - + -
126D ASP* 2.7 47.5 + - - +
127D ILE* 3.1 1.8 + - - -
129D ALA* 1.3 81.8 - - + +
131D ALA* 1.3 68.3 + - - +
132D ASN* 3.2 12.4 + - - +
192D MET* 5.5 0.7 - - - -
399D TYR* 3.6 36.8 - + - -
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Residues in contact with ALA 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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127D ILE* 2.7 26.1 + - + +
128D MET 5.0 2.5 - - - +
129D ALA 3.6 0.6 - - - -
130D PHE* 1.3 72.4 - - - +
132D ASN* 1.3 71.9 + - - +
133D SER* 4.1 7.3 - - - +
136D VAL* 4.0 29.6 - - + -
137D VAL 5.5 0.2 - - - +
192D MET* 4.0 29.3 - - + +
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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