Contacts of the helix formed by residues 118 - 123 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 4.7 0.7 - - - +
117B LEU* 1.3 87.1 - - + +
119B LEU* 1.3 67.3 + - - +
120B TYR* 3.2 26.5 - - + -
121B GLN* 2.9 42.0 + - - +
122B MET* 3.1 8.0 + - - +
309B HIS* 4.4 2.7 - - + -
347B PRO 3.9 7.4 - - - +
348B GLY* 3.2 30.5 - - - +
349B LYS 3.4 15.0 - - - +
350B PRO* 4.7 0.4 - - + -
351B GLY 3.6 2.2 - - - +
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Residues in contact with LEU 119 (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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108B TYR* 3.7 37.9 - - + +
112B ALA* 3.7 14.4 - - + -
117B LEU 3.4 1.2 + - - -
118B PRO* 1.3 70.7 - - - +
120B TYR* 1.3 64.0 + - - +
122B MET* 3.0 7.7 + - + -
123B LEU* 3.0 42.2 + - + +
275B ILE* 3.8 24.9 - - + -
306B ALA 4.7 1.6 - - - +
309B HIS* 3.7 21.0 + - + +
351B GLY 3.0 19.3 + - - +
352B LEU* 3.7 24.7 - - + -
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Residues in contact with TYR 120 (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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118B PRO* 3.2 28.8 - - + +
119B LEU* 1.3 76.1 - - - +
121B GLN* 1.3 81.8 + - + +
124B GLY 3.3 0.7 + - - -
125B GLY* 2.6 41.2 + - - -
127B ARG 3.3 28.7 - - - -
128B ASP* 3.5 23.6 + - + +
309B HIS* 3.0 50.5 + + - +
312B ALA* 4.1 4.9 - - + -
313B SER* 3.1 13.2 - - - +
346B MET* 3.5 25.5 + - + +
347B PRO 3.8 7.1 + - - -
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Residues in contact with GLN 121 (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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79A LEU 5.0 2.4 - - - +
80A ALA* 3.6 43.3 - - + +
82A TYR* 5.5 1.6 - - - +
111A TRP* 5.2 4.0 + - - -
114A MET* 6.2 0.2 - - - +
117B LEU* 3.8 16.3 - - + +
118B PRO* 2.9 33.8 + - + +
120B TYR* 1.3 111.9 + - + +
122B MET* 1.3 66.2 + - - +
123B LEU 3.1 0.4 - - - -
124B GLY* 3.2 11.3 + - - -
125B GLY* 3.7 7.7 + - - +
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Residues in contact with MET 122 (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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111A TRP* 3.8 23.6 + - + +
115A CYS* 4.6 4.7 - - - -
122A MET* 4.5 7.9 - - + -
111B TRP* 3.5 42.4 - - + +
112B ALA* 3.4 26.2 - - + +
115B CYS* 2.9 48.5 - - + -
117B LEU* 4.3 14.5 - - + +
118B PRO 3.1 9.8 + - - +
119B LEU* 3.0 17.4 + - + +
121B GLN* 1.3 78.7 - - - +
123B LEU* 1.3 60.7 + - + +
124B GLY 3.6 0.3 + - - -
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Residues in contact with LEU 123 (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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83A GLU* 4.8 0.9 - - - +
108B TYR* 4.1 21.5 - - + -
111B TRP* 4.8 5.4 - - + -
119B LEU* 3.0 38.7 + - + +
121B GLN 3.1 0.2 - - - -
122B MET* 1.3 85.9 - - + +
124B GLY* 1.3 54.7 + - - +
275B ILE* 4.1 16.8 - - + -
279B GLU* 3.7 23.8 - - - +
309B HIS 4.4 0.9 - - - +
310B PHE* 4.0 26.9 - - + -
313B SER* 3.3 19.1 + - - +
314B LYS* 2.9 30.4 + - - +
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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