Contacts of the helix formed by residues 121 - 129 (chain C) in PDB entry 3P9K
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C PHE* 2.9 20.5 + - + +
112C LEU* 4.2 10.1 - - + -
120C SER* 1.3 75.0 - - - +
122C ALA* 1.3 63.1 + - - +
123C ALA 3.2 2.2 - - - -
124C LEU* 3.1 23.4 + - + +
125C ALA* 3.3 8.1 + - - +
180C HIS* 3.6 30.3 - - + +
183C ILE* 4.4 21.3 - - + -
184C ILE* 4.9 5.2 - - + -
17D CYS* 4.1 20.4 - - - -
20D ALA* 4.3 17.7 - - + +
21D LEU* 3.5 42.0 - - + -
24D ALA* 3.8 6.6 - - + +
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ILE* 4.1 28.9 - - + +
112C LEU* 3.2 24.1 - - - +
114C PRO* 6.4 0.2 - - + -
120C SER* 3.0 18.2 + - - +
121C MET* 1.3 77.7 - - - +
123C ALA* 1.3 62.8 + - - +
125C ALA* 3.1 5.6 + - - +
126C LEU* 3.1 26.7 + - + +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER 3.9 1.6 + - - -
121C MET 3.2 1.0 - - - -
122C ALA* 1.3 80.0 - - - +
124C LEU* 1.3 56.5 + - - +
126C LEU* 3.3 12.4 + - + +
127C MET* 3.1 26.2 + - - +
172C VAL* 4.6 2.8 - - - +
175C GLU* 3.7 31.2 - - + +
176C GLY* 3.8 8.7 + - - +
179C ASN* 3.8 21.9 + - + +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER 5.1 0.2 + - - -
121C MET* 3.1 16.1 + - - +
123C ALA* 1.3 75.9 - - - +
125C ALA* 1.3 60.2 + - - +
127C MET* 3.5 28.6 - - + +
128C ASN* 2.9 38.1 + - - +
176C GLY* 3.7 22.9 - - - +
177C MET* 3.7 12.6 - - + -
179C ASN* 6.1 0.7 - - + -
180C HIS* 3.7 33.4 - - + +
263C TRP* 4.3 7.2 - - + -
603C CIY 4.2 13.2 - - + +
21D LEU* 4.1 16.8 - - + -
24D ALA* 3.9 9.9 - - + -
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 5.2 5.4 - - + -
34C LYS* 4.5 6.0 - - - +
37C ILE* 3.8 23.1 - - + -
112C LEU* 5.4 1.8 - - + -
121C MET 3.3 3.9 + - - +
122C ALA* 3.1 12.7 + - - +
124C LEU* 1.3 79.1 - - - +
126C LEU* 1.3 63.9 + - + +
129C GLN* 2.7 30.7 + - - +
23D LEU 5.1 1.3 - - - +
24D ALA* 3.5 27.5 - - + +
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 4.0 22.5 - - + +
37C ILE* 3.9 24.5 - - + -
38C GLU* 3.6 34.3 - - + +
122C ALA* 3.1 14.2 + - + +
123C ALA* 3.8 11.4 - - + +
124C LEU 3.3 0.4 - - - -
125C ALA* 1.3 78.3 - - - +
127C MET* 1.3 61.6 + - - +
129C GLN 3.9 0.9 - - - -
130C ASP* 3.2 24.4 + - - +
172C VAL* 4.1 9.9 - - + +
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Residues in contact with MET 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ALA 3.1 16.5 + - - +
124C LEU* 3.5 26.7 - - + +
125C ALA 3.2 0.2 - - - -
126C LEU* 1.3 75.8 - - - +
128C ASN* 1.3 88.2 + - - +
130C ASP* 3.0 19.2 + - - +
133C LEU* 3.4 24.3 - - + +
169C PHE* 4.7 2.7 - - + -
172C VAL* 3.6 25.1 - - + +
173C PHE* 3.6 37.2 - - + +
176C GLY* 4.7 0.9 - - - -
177C MET* 3.7 11.7 - - + -
603C CIY 3.5 26.2 - - + -
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 2.9 18.8 + - - +
127C MET* 1.3 88.9 - - - +
129C GLN* 1.3 78.1 + - - +
130C ASP 3.3 0.7 + - - -
133C LEU* 4.1 19.5 - - - +
134C MET* 3.9 13.7 - - - +
137C TRP* 5.3 2.4 + - - -
316C ILE* 3.6 27.1 - - + +
320C HIS* 5.4 0.5 + - - -
603C CIY 2.8 30.8 + - - +
24D ALA 3.0 17.2 + - - +
25D SER* 3.6 6.0 - - - -
27D SER* 4.0 5.2 + - - +
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Residues in contact with GLN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 3.9 25.8 - - + +
31C MET* 3.9 19.4 - - - +
34C LYS* 3.1 32.1 + - + +
125C ALA* 2.7 36.7 + - - +
126C LEU 3.9 1.1 - - - -
127C MET 3.2 1.0 - - - -
128C ASN* 1.3 77.4 - - - +
130C ASP* 1.3 64.5 + - - +
131C LYS 3.7 0.9 + - - -
134C MET* 4.0 7.0 - - - +
23D LEU 5.0 1.5 + - - -
24D ALA 3.1 22.4 + - - -
25D SER* 4.0 2.6 - - - -
26D SER 3.8 5.2 + - - -
27D SER* 2.8 38.2 + - - -
138D TYR* 3.7 9.7 - - - -
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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