Contacts of the helix formed by residues 121 - 129 (chain D) in PDB entry 3P9I
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 MET 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C CYS* 4.0 23.1 - - - +
20C ALA* 4.4 16.8 - - + +
21C LEU* 3.6 33.0 - - + -
24C ALA* 3.8 7.6 - - + +
111D PHE* 3.0 18.3 + - + +
112D LEU* 4.1 9.6 - - + +
120D SER* 1.3 76.9 - - - +
122D ALA* 1.3 62.8 - - - +
123D ALA 3.3 1.8 - - - -
124D LEU* 3.2 30.1 + - + +
125D ALA* 3.3 8.8 + - - +
180D HIS* 3.8 25.6 - - + +
183D ILE* 3.9 31.2 - - + -
184D ILE* 4.9 3.8 - - + -
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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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37D ILE* 4.0 29.1 - - + +
112D LEU* 3.4 23.7 - - - +
113D THR* 5.4 0.2 - - - -
114D PRO* 6.2 0.7 - - + -
120D SER* 3.1 17.2 + - - +
121D MET* 1.3 78.4 - - - +
123D ALA* 1.3 57.1 + - - +
125D ALA* 2.9 5.8 + - - +
126D LEU* 2.9 33.0 + - + +
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Residues in contact with ALA 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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120D SER 4.1 1.6 + - - -
121D MET 3.3 0.6 - - - -
122D ALA* 1.3 78.2 - - - +
124D LEU* 1.3 58.4 + - - +
126D LEU* 3.3 12.8 + - - +
127D MET* 3.0 27.4 + - - +
172D VAL* 4.8 2.1 - - - +
175D GLU* 3.8 9.6 - - + +
176D GLY* 3.7 25.6 + - - +
179D ASN* 3.7 31.1 + - + +
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Residues in contact with LEU 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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21C LEU* 4.0 11.9 - - + -
24C ALA* 4.0 11.0 - - + -
120D SER 5.7 0.7 - - - +
121D MET* 3.2 25.2 + - - +
122D ALA 3.1 0.8 - - - -
123D ALA* 1.3 75.7 - - + +
125D ALA* 1.3 60.8 + - - +
127D MET* 3.7 23.5 - - + +
128D ASN* 3.0 39.5 + - - +
176D GLY* 3.4 28.9 - - - +
177D MET* 4.1 8.3 - - + -
179D ASN* 5.9 0.2 - - + -
180D HIS* 3.9 32.5 - - + +
263D TRP* 4.5 2.2 - - + -
604D SNY 4.4 16.6 - - - +
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Residues in contact with ALA 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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24C ALA* 3.4 28.5 - - + +
33D LEU* 4.9 8.3 - - + -
34D LYS* 4.4 5.2 - - - +
37D ILE* 3.7 23.3 - - + -
112D LEU* 5.2 1.6 - - + -
121D MET 3.3 5.1 + - - +
122D ALA* 2.9 9.3 + - - +
124D LEU* 1.3 77.3 - - - +
126D LEU* 1.3 66.3 + - - +
129D GLN* 2.8 32.8 + - - +
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Residues in contact with LEU 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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34D LYS* 3.8 23.2 - - + +
37D ILE* 3.7 26.5 - - + -
38D GLU* 3.6 34.5 - - + +
122D ALA* 2.9 17.0 + - + +
123D ALA* 3.6 14.1 - - - +
125D ALA* 1.3 79.9 - - - +
127D MET* 1.3 60.8 + - - +
129D GLN 4.1 1.0 - - - -
130D ASP* 3.5 21.8 + - - +
172D VAL* 4.1 10.0 - - + +
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Residues in contact with MET 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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123D ALA 3.0 16.1 + - - +
124D LEU* 3.7 17.9 - - + +
125D ALA 3.2 0.2 - - - -
126D LEU* 1.3 76.0 - - - +
128D ASN* 1.3 93.1 + - - +
130D ASP* 3.0 19.4 + - - +
133D LEU* 3.4 20.0 - - + +
169D PHE* 4.2 4.2 - - + -
172D VAL* 3.7 18.8 - - + +
173D PHE* 3.7 34.8 - - - +
176D GLY* 4.7 1.1 - - - -
177D MET* 3.6 24.9 - - + -
604D SNY 3.6 27.6 - - + +
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Residues in contact with ASN 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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24C ALA 3.2 23.4 + - - +
25C SER* 3.7 5.8 - - - -
27C SER* 4.1 4.4 + - - +
124D LEU 3.0 21.8 + - - -
127D MET* 1.3 94.0 - - - +
129D GLN* 1.3 65.3 - - - +
130D ASP 3.2 2.6 + - - -
133D LEU* 3.9 18.8 - - - +
134D MET* 3.6 14.6 - - - +
137D TRP* 5.3 1.9 + - - -
316D ILE* 3.5 26.4 - - + +
320D HIS* 5.4 1.3 + - - -
604D SNY 2.9 28.8 + - - +
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Residues in contact with GLN 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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23C LEU 4.6 1.6 + - - -
24C ALA 2.9 26.4 + - - +
25C SER 4.0 0.3 - - - -
26C SER 3.9 0.5 + - - -
27C SER* 2.5 38.6 + - - -
138C TYR* 3.7 0.7 - - - -
30D PRO* 3.8 23.4 + - + +
31D MET* 3.7 33.3 - - - +
33D LEU* 6.3 0.2 - - - +
34D LYS* 2.8 35.6 + - + +
125D ALA* 2.8 35.8 + - - +
126D LEU 4.1 0.2 - - - -
127D MET 3.2 0.8 - - - -
128D ASN* 1.3 80.0 - - - +
130D ASP* 1.3 62.4 + - - +
134D MET* 3.9 7.4 - - - +
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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