Contacts of the helix formed by residues 118 - 123 (chain C) in PDB entry 1JPM
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 PRO 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLY 4.6 1.1 - - - +
117C LEU* 1.3 88.3 - - + +
119C LEU* 1.3 66.2 + - - +
120C TYR* 3.6 27.1 - - + -
121C GLN* 3.1 38.1 + - + +
122C MET* 3.2 8.0 + - - +
309C HIS* 4.4 1.8 - - + -
347C PRO 4.1 6.7 - - - +
348C GLY* 3.4 31.2 - - - +
349C LYS 3.5 16.8 - - - +
350C PRO* 3.9 1.5 - - + -
351C GLY 3.5 3.1 - - - +
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Residues in contact with LEU 119 (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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105C MET 5.4 0.7 - - - +
108C TYR* 3.7 26.2 - - + +
109C ASP 4.8 0.2 - - - +
112C ALA* 3.7 8.1 - - + -
117C LEU 3.4 1.8 + - - -
118C PRO* 1.3 70.6 - - - +
120C TYR* 1.3 64.0 + - - +
122C MET* 3.1 30.8 + - + +
123C LEU* 3.1 35.5 + - + +
275C ILE* 3.8 25.6 - - + -
306C ALA 5.0 0.7 - - - +
309C HIS* 3.7 15.9 + - + +
351C GLY* 2.8 25.1 + - - +
352C LEU* 3.7 23.8 - - + -
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Residues in contact with TYR 120 (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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118C PRO* 3.2 27.5 - - + -
119C LEU* 1.3 77.4 - - - +
121C GLN* 1.3 81.4 + - + +
123C LEU* 4.6 0.2 - - - -
124C GLY 3.2 1.4 + - - -
125C GLY* 2.6 41.3 + - - -
127C ARG 3.3 28.3 - - - -
128C ASP* 2.5 27.0 + - - -
309C HIS* 2.9 52.9 + + - +
312C ALA* 4.3 5.4 - - + -
313C SER* 3.1 13.5 - - - +
346C MET* 3.6 26.9 + - + +
347C PRO 3.9 6.8 + - - -
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Residues in contact with GLN 121 (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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117C LEU* 3.6 19.4 - - + +
118C PRO* 3.1 32.3 + - + +
120C TYR* 1.3 111.5 + - + +
122C MET* 1.3 65.8 + - - +
123C LEU 3.0 2.2 - - - -
124C GLY* 3.0 11.3 + - - -
125C GLY* 3.6 8.8 + - - +
128C ASP* 4.7 1.8 + - - -
79D LEU 5.0 2.8 - - - +
80D ALA* 3.6 41.1 + - - +
82D TYR* 5.3 2.1 - - - +
111D TRP* 5.2 4.0 + - - -
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Residues in contact with MET 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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108C TYR* 4.1 4.9 - - + +
111C TRP* 3.2 55.4 - - + +
112C ALA* 3.5 28.5 - - + +
115C CYS* 4.1 9.2 - - - -
117C LEU* 4.4 19.6 - - + +
118C PRO 3.2 10.9 + - - +
119C LEU* 3.1 33.5 + - + +
121C GLN* 1.3 77.3 - - - +
123C LEU* 1.3 64.7 + - + +
124C GLY 3.8 0.2 + - - -
111D TRP* 3.8 22.6 + - + +
122D MET* 4.5 12.8 - - + -
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Residues in contact with LEU 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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108C TYR* 4.1 25.8 - - + -
111C TRP* 5.5 2.0 - - + -
119C LEU* 3.1 38.4 + - + +
121C GLN 3.0 1.0 - - - -
122C MET* 1.3 84.8 - - + +
124C GLY* 1.3 55.0 + - - +
275C ILE* 4.2 14.6 - - + -
279C GLU* 3.4 22.4 - - - +
309C HIS 4.3 2.0 - - - +
310C PHE* 3.9 28.5 - - + -
313C SER* 3.3 18.5 - - - +
314C LYS* 2.9 30.7 + - - +
83D GLU* 4.8 0.7 - - - +
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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