Contacts of the helix formed by residues 132 - 140 (chain I) in PDB entry 1JJ2
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 LEU 132 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19I MET* 3.2 43.7 - - + -
41I ALA 3.5 24.9 - - - +
44I ALA* 3.1 28.1 + - + +
46I ILE* 3.9 20.0 - - + -
57I TYR* 5.9 0.7 - - + +
75I PRO* 3.7 25.8 - - + +
78I ILE* 4.6 9.1 - - + +
79I PHE* 3.9 9.9 - - + +
130I VAL 4.0 0.2 + - - -
131I THR* 1.3 71.2 - - - +
133I GLY* 1.3 63.0 + - - +
135I ILE* 3.0 15.4 + - + +
136I SER* 2.9 26.0 + - - -
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Residues in contact with GLY 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLU* 3.0 14.4 + - - +
75I PRO* 4.5 2.0 - - - -
131I THR* 2.9 12.5 - - - +
132I LEU* 1.3 78.4 - - - +
134I GLU* 1.3 60.4 + - - +
136I SER 3.3 0.2 + - - -
137I GLU* 3.0 32.7 + - - +
145I TRP* 3.7 27.3 - - - -
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Residues in contact with GLU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I GLU* 4.8 13.3 - - - +
129I PHE* 5.0 1.9 - - - +
130I VAL* 3.4 17.1 - - + +
131I THR* 2.9 43.1 + - + +
133I GLY* 1.3 76.8 - - - +
135I ILE* 1.3 63.7 + - - +
137I GLU* 3.1 17.6 + - - +
138I THR* 3.0 26.4 + - - -
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Residues in contact with ILE 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ILE* 4.2 11.2 - - + -
53I ILE* 4.1 24.9 - - + -
54I VAL* 4.7 13.0 - - + -
57I TYR* 4.3 26.7 - - + -
78I ILE* 5.5 5.6 - - + -
130I VAL* 3.8 15.5 - - + -
131I THR 3.0 13.6 + - - +
132I LEU* 3.0 28.6 + - + +
134I GLU* 1.3 76.1 - - - +
136I SER* 1.3 57.8 + - - +
138I THR* 3.1 9.1 + - - -
139I LEU* 2.9 49.9 + - + +
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Residues in contact with SER 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I LYS 2.7 28.0 + - - -
74I ARG 3.3 0.3 - - - -
75I PRO* 2.9 35.1 - - - +
78I ILE* 4.6 2.4 - - - +
132I LEU 2.9 9.9 + - - -
133I GLY 3.7 7.4 - - - -
135I ILE* 1.3 76.2 - - - +
137I GLU* 1.3 60.2 + - - +
139I LEU* 3.3 3.9 + - - +
140I GLY 3.1 4.7 + - - -
141I ALA* 2.8 37.1 + - - +
145I TRP* 3.8 3.6 - - - -
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Residues in contact with GLU 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28030 C 4.4 3.6 + - - -
133I GLY 3.0 18.9 + - - +
134I GLU* 3.1 19.0 + - - +
136I SER* 1.3 76.5 - - - +
138I THR* 1.3 64.1 + - - +
140I GLY* 3.2 13.0 + - - -
141I ALA* 4.6 8.3 - - - +
143I LYS* 3.7 38.4 + - + +
145I TRP* 4.2 11.6 + - + -
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Residues in contact with THR 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27730 G 6.0 2.2 - - - +
28030 C 4.1 16.6 + - - +
50I GLU* 4.8 6.8 + - - -
54I VAL* 3.6 39.1 - - + +
58I GLU* 4.3 14.5 - - + +
134I GLU 3.0 13.8 + - - -
135I ILE 3.4 9.6 - - - -
137I GLU* 1.3 79.3 - - - +
139I LEU* 1.3 61.4 + - + +
140I GLY 3.2 0.7 + - - -
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Residues in contact with LEU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28030 C 3.8 14.4 - - - +
28040 C 4.6 0.9 + - - -
54I VAL* 4.9 1.6 - - + +
57I TYR* 4.2 12.8 - - + +
58I GLU* 3.6 44.2 - - + +
61I VAL* 4.3 15.4 - - + +
71I TYR* 5.3 0.4 - - + -
72I PRO 4.5 2.0 - - - +
73I LYS* 3.9 50.8 + - + +
78I ILE* 4.4 9.0 - - + -
135I ILE* 2.9 35.2 + - + +
136I SER* 3.3 6.7 + - - +
138I THR* 1.3 77.6 - - + +
140I GLY* 1.3 57.2 + - - +
141I ALA 3.5 0.2 - - - -
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Residues in contact with GLY 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28030 C 3.2 30.3 - - - -
28040 C 3.6 20.9 + - - +
73I LYS* 5.2 3.4 - - - -
136I SER 3.1 1.6 + - - -
137I GLU 3.2 4.4 + - - -
138I THR 3.1 5.1 - - - -
139I LEU* 1.3 79.6 - - - +
141I ALA* 1.3 69.8 + - - +
142I ASN* 3.7 0.5 + - - -
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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