Contacts of the helix formed by residues 132 - 148 (chain D) in PDB entry 4DHI
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 ASN 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D GLN* 2.8 26.2 + - + +
131D THR* 1.3 79.6 + - - +
133D GLU* 1.3 65.2 + - - +
134D ALA* 3.9 8.1 + - - +
135D GLN* 3.3 33.3 + - + +
136D ALA 3.1 17.3 + - - -
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Residues in contact with GLU 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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128D GLN 4.2 0.7 - - - -
129D TRP* 3.4 33.1 + - + +
130D LYS 4.7 2.4 + - - +
131D THR 3.9 1.0 - - - -
132D ASN* 1.3 74.8 - - - +
134D ALA* 1.3 63.1 + - - +
136D ALA* 3.2 3.3 + - - +
137D ILE* 2.9 48.0 + - + +
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Residues in contact with ALA 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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132D ASN* 3.2 7.8 - - - +
133D GLU* 1.3 78.7 - - - +
135D GLN* 1.3 61.8 + - - +
137D ILE* 3.5 7.0 + - - +
138D GLU* 3.2 29.0 + - + +
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Residues in contact with GLN 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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128D GLN* 3.9 20.2 - - - +
132D ASN* 3.1 32.7 + - + +
134D ALA* 1.3 78.9 - - - +
136D ALA* 1.3 58.1 + - - +
138D GLU* 3.2 9.3 + - - +
139D THR* 3.0 44.0 + - - +
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Residues in contact with ALA 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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76D TYR* 3.6 8.0 - - - -
128D GLN* 3.6 18.1 - - - +
129D TRP* 3.6 52.5 - - + +
132D ASN 3.1 9.2 + - - +
133D GLU 3.6 7.0 - - - +
135D GLN* 1.3 77.1 - - - +
137D ILE* 1.3 57.9 + - - +
139D THR 3.3 1.4 + - - -
140D ALA* 2.8 28.6 + - - +
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Residues in contact with ILE 137 (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 PRO* 4.1 16.8 - - + -
129D TRP* 4.1 19.7 - - + -
133D GLU* 2.9 44.4 + - + +
134D ALA* 3.9 5.6 - - - +
136D ALA* 1.3 74.8 - - - +
138D GLU* 1.3 67.1 + - - +
140D ALA* 3.2 7.7 + - - +
141D ARG* 2.8 55.5 + - - +
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Residues in contact with GLU 138 (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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134D ALA* 3.2 19.6 + - + +
135D GLN* 3.9 11.7 - - - +
137D ILE* 1.3 80.5 - - - +
139D THR* 1.3 56.2 + - - +
141D ARG* 3.3 32.3 + - - +
142D ALA* 2.9 28.8 + - - +
145D ARG* 4.7 6.6 + - - -
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Residues in contact with THR 139 (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 TYR* 3.7 29.6 - - + -
128D GLN* 4.5 2.3 + - - -
135D GLN* 3.0 33.9 + - - +
136D ALA 3.6 4.7 - - - -
138D GLU* 1.3 75.6 - - - +
140D ALA* 1.3 59.2 + - - +
142D ALA* 3.2 5.3 + - - -
143D TRP* 2.8 53.4 + - + +
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Residues in contact with ALA 140 (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 PRO* 3.7 20.6 - - + -
47D PHE* 3.7 9.5 - - + -
76D TYR* 3.7 30.2 - - + +
129D TRP* 3.9 7.6 - - + -
136D ALA 2.8 17.4 + - - +
137D ILE 3.6 5.2 - - - +
139D THR* 1.3 74.9 - - - +
141D ARG* 1.3 57.3 + - - +
143D TRP* 3.5 1.6 + - - +
144D THR* 2.9 33.9 + - - -
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Residues in contact with ARG 141 (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 4.8 5.5 + - - -
45D SER 3.7 19.0 + - - -
46D PRO* 3.6 30.6 + - + +
48D GLU* 5.2 6.7 + - - +
137D ILE* 2.8 34.2 + - - +
138D GLU* 3.7 26.8 + - - +
139D THR 3.2 0.2 - - - -
140D ALA* 1.3 76.5 - - - +
142D ALA* 1.3 61.6 + - - +
144D THR* 3.2 5.0 + - - -
145D ARG* 3.1 38.2 + - - +
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Residues in contact with ALA 142 (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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138D GLU 2.9 17.2 + - - +
139D THR* 3.2 7.6 + - - +
141D ARG* 1.3 78.0 - - - +
143D TRP* 1.3 61.5 + - + +
145D ARG* 3.3 28.1 + - - +
146D LEU* 2.9 30.1 + - + +
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Residues in contact with TRP 143 (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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74D LYS* 4.1 20.6 - - + +
75D ILE* 3.5 30.1 - - - -
76D TYR* 3.5 44.6 - + + +
139D THR* 2.8 39.6 + - + +
140D ALA 3.8 4.3 - - - +
142D ALA* 1.3 75.7 - - + +
144D THR* 1.3 58.9 + - - +
146D LEU* 4.2 6.2 - - + +
147D TYR* 2.9 62.3 + + + +
148D ALA* 4.7 0.3 - - - +
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Residues in contact with THR 144 (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 PRO 3.5 13.6 + - - -
47D PHE* 3.5 23.8 - - - +
48D GLU 3.9 4.7 - - - +
50D GLY* 3.6 33.7 - - - +
52D PHE* 4.0 5.2 - - + -
140D ALA 2.9 18.8 + - - -
141D ARG* 3.2 9.4 + - - -
143D TRP* 1.3 76.3 - - - +
145D ARG* 1.3 60.0 + - - +
148D ALA* 2.9 32.6 + - + +
149D MET* 3.5 17.1 + - + +
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Residues in contact with ARG 145 (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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138D GLU* 4.7 7.7 + - - -
141D ARG* 3.1 21.9 + - - +
142D ALA* 3.6 40.7 + - - +
144D THR* 1.3 78.6 - - - +
146D LEU* 1.3 61.6 + - - +
149D MET* 3.9 39.8 + - + +
150D ASN* 5.2 2.3 + - - +
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Residues in contact with LEU 146 (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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142D ALA* 2.9 17.3 + - + +
143D TRP* 3.9 9.0 - - + +
145D ARG* 1.3 79.0 - - - +
147D TYR* 1.3 99.9 + - + +
149D MET 5.2 0.2 - - - -
150D ASN 5.8 0.9 + - - -
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Residues in contact with TYR 147 (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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73D THR* 3.5 13.6 - - + +
74D LYS* 3.8 51.1 - - + +
143D TRP* 2.9 55.0 + + + +
146D LEU* 1.3 113.4 - - + +
148D ALA* 1.3 61.5 + - - +
149D MET 3.5 2.5 - - - -
150D ASN 5.3 0.9 - - - -
151D ASN* 3.9 14.4 - - - +
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Residues in contact with ALA 148 (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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49D GLY 4.2 0.7 - - - +
50D GLY* 3.3 10.6 - - - -
51D THR* 2.8 39.3 + - - +
52D PHE* 3.6 37.7 - - + -
73D THR* 4.0 3.6 - - + -
143D TRP 4.7 0.7 - - - +
144D THR* 2.9 16.2 + - - +
147D TYR* 1.3 77.7 - - + +
149D MET* 1.3 60.4 + - - +
151D ASN* 3.2 11.6 - - - +
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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