Contacts of the helix formed by residues 130 - 147 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 2.8 23.1 + - + +
129B SER* 1.3 81.6 + - - +
131B LYS* 1.3 58.8 + - - +
132B GLU* 3.7 9.5 + - - +
133B LYS* 3.2 41.1 + - + +
134B TYR 3.0 21.3 + - - -
136B ARG* 5.6 0.2 + - - -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASP* 6.0 0.4 + - - -
126B ILE 3.9 0.2 + - - -
127B TYR* 3.3 59.8 + - + +
129B SER 4.1 0.2 - - - -
130B ASP* 1.3 71.8 + - - +
132B GLU* 1.3 60.6 + - - +
134B TYR* 3.2 5.7 + - + +
135B ASN* 2.9 49.7 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.3 8.1 - - - +
131B LYS* 1.3 78.5 - - - +
133B LYS* 1.3 56.5 + - - +
135B ASN* 3.4 8.8 + - - +
136B ARG* 2.4 62.6 + - - +
139B ARG* 5.0 0.9 + - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 4.0 24.5 - - + +
130B ASP* 3.2 37.7 + - + +
132B GLU* 1.3 76.6 - - - +
134B TYR* 1.3 65.4 + - - +
136B ARG* 3.3 30.7 + - - +
137B HIS* 3.0 54.3 + - + -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 5.3 1.3 - - + -
45B TYR* 2.6 30.1 + + - -
74B TYR* 3.7 21.7 + + - -
76B PRO* 3.3 21.4 - - + +
113B PRO* 3.5 10.6 - - + +
123B ILE* 3.6 26.2 - - + -
126B ILE* 3.8 8.7 - - + +
127B TYR* 3.7 52.0 - + + -
130B ASP 3.0 13.7 + - - +
131B LYS* 3.2 10.3 + - + +
133B LYS* 1.3 75.7 - - - +
135B ASN* 1.3 76.0 + - - +
137B HIS* 3.2 4.4 + - - +
138B ALA* 2.9 33.8 + - + +
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.9 19.0 - - + +
127B TYR* 5.7 0.3 - - - -
131B LYS* 2.9 37.7 + - - +
132B GLU* 3.8 7.3 - - - +
134B TYR* 1.3 92.3 - - - +
136B ARG* 1.3 57.8 + - - +
138B ALA* 3.9 0.5 - - - +
139B ARG* 3.0 51.8 + - - +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 5.6 0.2 + - - -
132B GLU* 2.4 51.9 + - - +
133B LYS* 3.5 38.5 - - - +
134B TYR 3.3 0.2 - - - -
135B ASN* 1.3 76.4 - - - +
137B HIS* 1.3 66.6 + - + +
139B ARG* 3.4 24.1 + - - +
140B GLU* 2.9 56.4 + - + +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TYR* 3.2 43.8 + + + -
126B ILE* 4.8 3.0 - - + +
133B LYS* 3.0 56.0 + - + +
134B TYR 3.6 2.5 - - - +
136B ARG* 1.3 84.6 + - + +
138B ALA* 1.3 60.8 + - - +
140B GLU* 3.4 19.4 + - - +
141B TRP* 3.0 38.1 + + + +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 3.8 19.5 - - + -
45B TYR* 3.7 31.0 - - + +
74B TYR* 3.8 17.0 - - + +
134B TYR* 2.9 25.1 + - + +
137B HIS* 1.3 73.2 - - - +
139B ARG* 1.3 53.2 + - - +
141B TRP* 3.5 1.7 + - - +
142B THR* 2.8 36.8 + - - -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER 5.8 0.2 - - - -
44B ALA* 3.2 30.5 - - - +
46B GLN* 5.9 7.0 - - + +
132B GLU 5.0 1.0 + - - -
135B ASN* 3.0 48.0 + - - +
136B ARG* 3.7 22.8 + - - +
138B ALA* 1.3 74.8 - - - +
140B GLU* 1.3 64.8 + - + +
142B THR* 3.2 3.5 + - - -
143B GLN* 3.0 42.2 + - - +
15D ARG 6.0 1.8 - - - -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 2.9 41.8 + - + +
137B HIS* 3.4 23.9 + - - +
139B ARG* 1.3 77.4 - - + +
141B TRP* 1.3 63.1 + - + +
143B GLN* 3.4 12.9 + - - +
144B LYS* 2.9 29.4 + - - +
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Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 3.4 44.8 - - + +
73B ILE* 3.5 19.5 - - - -
74B TYR* 3.4 53.5 - + + +
123B ILE* 5.3 4.7 - - + -
137B HIS* 3.0 25.4 + - - +
138B ALA 4.0 1.3 - - - +
140B GLU* 1.3 79.7 - - + +
142B THR* 1.3 60.7 + - - +
144B LYS* 4.3 3.8 - - + -
145B TYR* 2.9 53.8 + + + +
146B ALA* 4.8 0.2 - - - +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA 3.6 3.8 + - - +
45B TYR* 3.5 37.5 - - - +
46B GLN 4.2 0.2 - - - +
48B GLY* 3.5 29.8 - - - -
50B PHE* 4.2 7.2 - - + -
138B ALA 2.8 22.9 + - - -
139B ARG* 3.2 5.8 + - - -
141B TRP* 1.3 75.5 - - - +
143B GLN* 1.3 57.6 + - - +
146B ALA* 2.9 31.8 + - - -
147B MET* 3.2 23.6 + - + +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ARG* 3.0 35.2 + - - +
140B GLU* 3.7 12.0 - - - +
142B THR* 1.3 76.0 - - - +
144B LYS* 1.3 63.0 + - - +
147B MET* 3.8 44.0 + - + +
14D GLN* 4.0 38.0 + - + +
15D ARG* 4.7 5.1 - - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLU 2.9 18.8 + - - +
141B TRP* 3.9 6.3 - - + +
143B GLN* 1.3 79.3 - - - +
145B TYR* 1.3 103.6 + - + +
147B MET 4.7 3.8 - - - +
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 3.7 11.0 - - - +
72B LYS* 3.5 65.7 - - + +
141B TRP* 2.9 52.8 + + + +
144B LYS* 1.3 116.6 + - + +
146B ALA* 1.3 60.2 + - - +
147B MET 3.7 3.1 - - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 3.4 5.1 - - - -
49B VAL* 2.8 47.5 + - - +
50B PHE* 3.6 36.8 - - + -
71B THR* 3.9 4.3 - - + -
72B LYS 4.7 1.3 - - - +
141B TRP 3.8 0.2 + - - -
142B THR* 2.9 16.2 + - - +
145B TYR* 1.3 78.7 - - - +
147B MET* 1.3 59.4 + - - +
22D SER* 4.1 1.4 + - - -
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Residues in contact with MET 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN 3.5 25.4 - - - +
47B GLY* 3.6 21.5 - - - +
48B GLY* 4.4 0.2 - - - -
49B VAL* 5.8 0.4 - - - -
142B THR* 3.2 25.0 + - + +
143B GLN* 3.8 26.9 + - + +
144B LYS 4.7 4.2 - - - +
145B TYR 4.9 1.6 - - - +
146B ALA* 1.3 80.3 + - - +
13D LEU* 5.8 0.9 - - - -
14D GLN* 3.5 61.9 - - + +
17D PRO* 5.2 1.3 - - + -
22D SER* 4.1 7.1 + - - +
23D ALA* 3.6 8.8 - - - +
24D GLY* 3.3 30.3 + - - +
25D PRO* 5.1 5.5 - - - +
34D GLN* 4.8 2.6 - - - +
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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