Contacts of the helix formed by residues 113 - 130 (chain D) in PDB entry 3NDR
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 LEU 113 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TRP* 4.0 19.9 - - + -
109A ILE* 4.4 11.4 - - + -
113A LEU* 3.7 29.8 - - + -
156A ALA* 4.6 2.9 - - + +
109D ILE* 3.0 22.8 + - + +
111D VAL 3.0 0.4 + - - -
112D ASN* 1.3 79.7 - - - +
114D THR* 1.3 67.2 + - + +
115D GLY 3.1 0.9 - - - -
116D THR* 3.0 15.1 + - - +
117D PHE* 3.1 9.9 + - - +
157D ALA* 4.0 18.8 - - + +
160D GLY* 3.6 38.1 - - - +
161D VAL* 3.7 9.2 - - + +
164D PHE* 5.2 2.6 - - + -
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Residues in contact with THR 114 (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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102A LEU* 4.5 6.2 - - - +
105A TRP* 2.9 36.0 - - + +
106A ARG* 4.9 9.2 + - + -
109A ILE* 4.8 7.4 - - + -
109D ILE* 2.9 30.0 + - + +
110D ASP* 3.5 24.5 + - - +
113D LEU* 1.3 74.3 - - + +
115D GLY* 1.3 57.8 + - - +
117D PHE* 3.2 2.6 + - - +
118D ILE* 2.9 39.0 + - - +
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.3 37.1 - - - +
63D SER* 4.0 3.6 - - - -
110D ASP 2.7 17.3 + - - -
111D VAL 3.2 12.0 + - - -
113D LEU 3.1 0.8 - - - -
114D THR* 1.3 75.1 - - - +
116D THR* 1.3 62.3 + - - +
118D ILE* 3.4 0.4 + - - -
119D VAL* 3.2 23.2 + - - +
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Residues in contact with THR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 4.6 7.6 - - + -
87D ASN* 4.0 28.3 + - + +
89D ALA 5.1 4.0 - - - +
90D SER* 5.3 0.2 - - - +
111D VAL 3.9 2.2 - - - +
112D ASN* 2.6 36.8 - - - +
113D LEU* 3.0 6.6 + - - +
115D GLY* 1.3 75.2 - - - +
117D PHE* 1.3 55.7 + - - +
119D VAL* 3.5 0.6 + - - -
120D THR* 2.5 39.5 + - - -
138D SER* 5.1 0.9 + - - -
161D VAL* 3.8 20.0 - - + +
164D PHE* 4.2 12.0 - - - -
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Residues in contact with PHE 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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97A TRP* 3.8 15.9 - + - -
100A VAL* 3.7 30.1 - - + -
101A ASP 3.7 15.0 - - - -
102A LEU* 3.7 28.9 - - + -
105A TRP* 3.6 56.1 - + + -
113D LEU 3.1 5.9 + - - -
114D THR 3.2 8.0 + - - +
116D THR* 1.3 75.5 + - - +
118D ILE* 1.3 65.1 + - + +
120D THR 3.0 0.2 + - - -
121D ARG* 2.8 54.5 + - + +
164D PHE* 4.0 21.1 - + + -
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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
----------------------------------------------------------
102A LEU* 4.1 26.9 - - + -
106A ARG* 4.8 2.2 - - - +
62D ILE 3.6 14.8 - - - +
63D SER* 3.5 28.5 - - - +
65D PRO* 4.1 24.0 - - + -
68D VAL* 3.7 23.1 - - + +
114D THR* 2.9 26.9 + - - +
115D GLY 3.6 7.0 - - - +
116D THR 3.4 0.2 - - - -
117D PHE* 1.3 81.2 - - + +
119D VAL* 1.3 62.1 + - - +
121D ARG* 3.6 5.6 - - - +
122D ALA* 3.3 20.3 + - - +
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Residues in contact with VAL 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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11D LEU* 4.4 6.5 - - + -
13D THR* 4.5 6.1 - - + -
62D ILE* 3.8 28.0 - - + -
68D VAL* 3.9 24.0 - - + -
72D PHE* 3.5 16.5 - - + -
85D LEU* 3.9 18.8 - - + +
87D ASN* 3.6 20.9 - - - +
115D GLY 3.2 16.9 + - - +
116D THR* 4.0 0.4 - - - +
118D ILE* 1.3 74.6 - - - +
120D THR* 1.3 56.5 + - - +
122D ALA 3.1 1.0 + - - -
123D GLY* 2.7 32.2 + - - -
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 5.2 0.7 - - + -
85D LEU* 3.9 7.9 - - + -
87D ASN* 3.1 19.6 + - - -
116D THR 2.5 24.6 + - - -
117D PHE 3.0 1.3 + - - -
119D VAL* 1.3 74.2 - - - +
121D ARG* 1.3 55.1 + - - +
124D THR* 2.8 53.0 + - + +
136D VAL* 4.3 11.0 - - + -
164D PHE* 3.7 19.4 - - + -
168D LEU* 3.4 33.9 - - + -
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 2.8 52.2 + - - +
98A ASP* 3.2 30.7 + - - +
100A VAL 3.1 26.4 + - - -
101A ASP 5.9 0.2 - - - -
117D PHE* 2.8 37.3 + - + +
118D ILE* 3.6 7.6 - - - +
120D THR* 1.3 77.9 - - - +
122D ALA* 1.3 59.3 + - + +
124D THR* 3.4 2.7 + - - -
125D ASP* 2.9 69.9 + - - +
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Residues in contact with ALA 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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68D VAL* 4.2 7.0 - - + +
69D LYS* 5.8 7.9 - - + -
72D PHE* 3.4 33.3 - - + +
118D ILE 3.3 10.9 + - - +
119D VAL 3.1 1.8 + - - -
121D ARG* 1.3 79.5 - - + +
123D GLY* 1.3 61.4 + - - +
125D ASP* 3.5 8.2 + - - +
126D GLN* 3.0 27.2 + - - +
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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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72D PHE* 3.3 26.8 - - - -
82D ILE* 3.8 6.4 - - - +
85D LEU* 4.5 8.3 - - - -
119D VAL 2.7 17.2 + - - -
120D THR 4.0 0.2 - - - -
122D ALA* 1.3 71.1 - - - +
124D THR* 1.3 59.9 + - - +
126D GLN* 3.1 5.5 + - - +
127D MSE 3.0 33.9 + - - +
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Residues in contact with THR 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 4.2 13.3 + - - -
85D LEU* 5.3 1.3 - - + -
120D THR* 2.8 38.6 + - + +
121D ARG* 3.4 5.5 + - - -
123D GLY* 1.3 71.6 - - - +
125D ASP* 1.3 66.7 + - - +
127D MSE 3.7 11.5 - - + +
128D ARG* 2.8 34.9 + - - +
136D VAL* 3.8 17.3 - - + -
168D LEU* 4.7 0.2 - - + -
172D LEU* 3.7 32.5 - - + -
177D ILE* 4.3 3.6 - - - +
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Residues in contact with ASP 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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97A TRP* 4.7 0.2 + - - -
121D ARG* 2.9 60.1 + - - +
122D ALA* 3.6 7.9 - - - +
124D THR* 1.3 84.0 + - - +
126D GLN* 1.3 57.7 + - - +
128D ARG* 3.2 17.0 + - - +
129D ALA* 2.8 32.7 + - - +
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Residues in contact with GLN 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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72D PHE* 3.0 48.8 + - + +
75D ILE* 4.1 5.9 - - - +
76D GLN* 3.1 34.6 + - + +
81D GLY* 3.4 8.7 - - - -
82D ILE* 3.1 29.9 + - + +
122D ALA 3.0 14.5 + - - +
123D GLY* 3.1 11.4 + - - +
125D ASP* 1.3 74.5 - - - +
127D MSE 1.3 63.4 + - - +
129D ALA* 3.5 6.2 + - - +
130D ALA* 3.1 22.9 + - - +
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Residues in contact with MSE 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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82D ILE* 3.2 37.9 - - + +
83D ASP 3.6 12.3 - - - +
85D LEU* 3.7 20.4 - - + +
123D GLY 3.0 18.7 + - - +
124D THR* 3.7 10.8 - - - +
126D GLN* 1.3 76.2 - - - +
128D ARG* 1.3 64.1 + - - +
130D ALA* 3.1 3.1 + - - -
131D GLY 3.1 4.0 + - - -
132D LYS* 2.9 37.2 + - + +
134D GLY* 3.4 24.0 - - - -
135D ARG 3.6 24.0 - - - +
136D VAL* 4.3 4.9 - - + -
177D ILE* 3.8 24.7 - - + -
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Residues in contact with ARG 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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97A TRP* 3.8 12.7 - - - +
98A ASP* 2.4 41.0 + - - -
121D ARG* 4.0 5.1 - - - +
124D THR* 2.8 21.5 + - - +
125D ASP* 3.4 12.6 + - - +
127D MSE 1.3 77.0 - - - +
129D ALA* 1.3 58.7 + - - +
131D GLY* 2.9 20.8 + - - -
132D LYS 5.1 1.1 - - - -
172D LEU* 4.4 6.6 - - - +
175D TYR* 3.0 69.4 + - + -
177D ILE* 4.7 7.6 - - - -
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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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76D GLN* 5.4 4.9 - - - +
125D ASP 2.8 20.4 + - - +
126D GLN* 3.9 6.3 - - - +
128D ARG* 1.3 74.6 - - - +
130D ALA* 1.3 55.6 + - - +
131D GLY 3.2 2.7 + - - -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN* 4.3 5.4 - - - +
80D GLY 3.6 22.9 - - - +
81D GLY* 4.9 0.9 - - - -
126D GLN 3.1 17.7 + - - +
127D MSE 3.1 0.4 + - - +
129D ALA* 1.3 75.3 - - - +
131D GLY* 1.3 63.2 + - - +
132D LYS* 3.1 26.2 + - + +
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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