Contacts of the helix formed by residues 130 - 147 (chain D) in PDB entry 4QPL
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 ASP 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D ILE* 2.7 22.2 + - + +
129D SER* 1.3 78.9 - - - +
131D LYS* 1.3 61.4 + - - +
132D GLU* 3.8 10.1 + - - +
133D LYS* 3.2 40.7 + - + +
134D TYR 2.9 23.6 + - - -
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Residues in contact with LYS 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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112D ASP* 5.9 1.0 + - - -
126D ILE 3.9 0.2 + - - -
127D TYR* 3.1 61.9 + - + +
129D SER 4.0 0.8 - - - -
130D ASP* 1.3 71.6 + - - +
132D GLU* 1.3 60.7 + - - +
134D TYR* 3.4 5.8 - - + +
135D ASN* 2.8 47.5 + - - +
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Residues in contact with GLU 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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130D ASP* 3.3 8.8 + - - +
131D LYS* 1.3 79.2 - - - +
133D LYS* 1.3 60.4 + - - +
135D ASN* 3.7 7.2 - - - +
136D ARG* 2.9 50.2 + - - +
139D ARG* 4.8 7.3 + - - +
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Residues in contact with LYS 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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126D ILE* 3.9 26.4 - - + +
130D ASP* 3.2 35.1 + - + +
132D GLU* 1.3 83.0 + - - +
134D TYR* 1.3 64.9 + - - +
136D ARG* 3.3 25.1 + - - +
137D HIS* 2.9 56.5 + - + +
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Residues in contact with TYR 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 ALA* 5.4 0.7 - - + -
45D TYR* 2.6 30.2 + + - -
74D TYR* 3.6 24.6 + + - -
76D PRO* 3.4 18.9 - - + +
113D PRO* 3.6 11.1 - - + +
123D ILE* 3.8 25.1 - - + -
126D ILE* 3.8 13.3 - - + +
127D TYR* 3.6 47.1 - + + -
130D ASP 2.9 13.5 + - - +
131D LYS* 3.4 13.5 - - + +
133D LYS* 1.3 75.7 - - - +
135D ASN* 1.3 75.9 + - - +
137D HIS* 3.1 4.7 + - - +
138D ALA* 2.8 34.2 + - + +
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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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44D ALA* 3.7 23.0 + - + +
131D LYS* 2.8 37.1 + - - +
132D GLU* 3.7 6.1 - - - +
134D TYR* 1.3 88.3 - - - +
136D ARG* 1.3 62.4 + - - +
138D ALA* 3.3 1.3 + - - +
139D ARG* 2.9 39.8 + - - +
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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
----------------------------------------------------------
132D GLU* 2.9 37.8 + - - +
133D LYS* 3.5 32.7 - - - +
135D ASN* 1.3 77.3 - - - +
137D HIS* 1.3 76.8 + - - +
139D ARG* 3.4 25.0 + - - +
140D GLU* 3.0 56.2 + - + +
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Residues in contact with HIS 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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74D TYR* 3.2 45.1 + + + -
126D ILE* 4.6 3.1 - - + +
133D LYS* 2.9 56.2 + - + +
134D TYR 3.6 2.2 - - - +
136D ARG* 1.3 91.0 + - - +
138D ALA* 1.3 59.1 + - - +
140D GLU* 3.4 19.6 + - - +
141D TRP* 3.0 39.4 + - + +
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Residues in contact with ALA 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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44D ALA* 3.7 23.8 - - + -
45D TYR* 3.9 26.1 - - + +
74D TYR* 3.8 16.5 - - + +
134D TYR* 2.8 24.8 + - + +
135D ASN* 3.7 1.3 - - - +
137D HIS* 1.3 73.6 - - - +
139D ARG* 1.3 57.5 + - - +
141D TRP* 3.9 1.7 - - - +
142D THR* 2.8 32.9 + - - -
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Residues in contact with ARG 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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15B ARG* 5.9 3.1 - - - +
44D ALA* 3.4 27.1 - - - +
46D GLN* 5.7 8.5 - - + +
132D GLU* 4.8 7.9 + - - -
135D ASN* 2.9 22.2 + - - +
136D ARG* 3.6 36.9 + - - +
138D ALA* 1.3 73.9 - - - +
140D GLU* 1.3 61.6 + - + +
142D THR* 3.2 3.8 + - - -
143D GLN* 2.9 49.7 + - - +
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Residues in contact with GLU 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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136D ARG* 3.0 51.5 + - + +
137D HIS* 3.4 24.2 + - - +
139D ARG* 1.3 77.4 - - + +
141D TRP* 1.3 64.2 + - + +
143D GLN* 3.3 12.5 + - - +
144D LYS* 2.9 29.0 + - - +
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Residues in contact with TRP 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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72D LYS* 3.5 45.9 - - + +
73D ILE* 3.6 17.3 - - - -
74D TYR* 3.5 55.2 - + + +
123D ILE* 5.4 4.9 - - + -
137D HIS* 3.0 28.3 + + + +
138D ALA 4.1 1.3 - - - +
140D GLU* 1.3 79.7 - - + +
142D THR* 1.3 61.2 + - - +
144D LYS* 4.3 2.7 - - + -
145D TYR* 2.9 52.9 + + + +
146D ALA* 4.8 0.3 - - - +
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Residues in contact with THR 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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44D ALA 3.5 3.7 + - - +
45D TYR* 3.5 37.8 - - - +
46D GLN 4.3 0.4 - - - +
48D GLY* 3.6 29.4 - - - -
50D PHE* 4.1 7.2 - - + -
138D ALA 2.8 19.5 + - - -
139D ARG* 3.2 9.8 + - - -
141D TRP* 1.3 75.3 - - - +
143D GLN* 1.3 58.6 + - - +
146D ALA* 2.9 28.6 + - - -
147D MET* 3.2 24.7 + - + +
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Residues in contact with GLN 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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14B GLN* 4.1 39.7 + - + +
15B ARG* 4.9 2.4 - - - +
139D ARG* 2.9 39.0 + - - +
140D GLU* 3.6 11.4 - - - +
141D TRP 3.2 0.2 - - - -
142D THR* 1.3 77.3 - - - +
144D LYS* 1.3 62.9 + - - +
147D MET* 3.7 44.9 + - + +
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Residues in contact with LYS 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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140D GLU 2.9 17.7 + - - +
141D TRP* 4.3 4.0 - - + -
142D THR 3.3 0.4 - - - -
143D GLN* 1.3 80.2 - - - +
145D TYR* 1.3 104.8 + - + +
147D MET 4.8 3.8 - - - +
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Residues in contact with TYR 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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71D THR* 3.7 11.6 - - - +
72D LYS* 3.7 65.5 - - + +
141D TRP* 2.9 45.8 + + + +
144D LYS* 1.3 122.4 + - + +
146D ALA* 1.3 59.5 + - - +
147D MET 3.7 2.5 - - - -
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Residues in contact with ALA 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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22B SER* 3.8 2.8 + - - -
48D GLY* 3.4 4.1 - - - -
49D VAL* 2.8 46.8 + - - +
50D PHE* 3.6 36.3 - - + -
71D THR* 3.9 3.6 - - + -
72D LYS 4.9 1.1 - - - +
141D TRP 4.8 0.2 - - - +
142D THR* 2.9 16.3 + - - +
145D TYR* 1.3 78.0 - - - +
147D MET* 1.3 59.8 + - - +
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Residues in contact with MET 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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13B LEU* 5.6 1.1 - - - -
14B GLN* 3.5 59.0 - - - +
17B PRO* 5.1 0.9 - - + -
22B SER* 4.0 7.4 + - - +
23B ALA* 3.6 9.2 - - - +
24B GLY* 3.4 30.1 + - - +
25B PRO* 5.0 6.1 - - - +
34B GLN* 4.7 4.2 - - - +
46D GLN 3.6 24.0 - - - +
47D GLY* 3.5 22.7 - - - +
48D GLY* 4.3 0.2 - - - -
142D THR* 3.2 25.7 + - + +
143D GLN* 3.7 31.5 + - + +
144D LYS 4.8 3.8 - - - +
145D TYR 5.0 1.0 - - - -
146D ALA* 1.3 80.5 + - - +
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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