Contacts of the helix formed by residues 141 - 150 (chain H) 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 ASN 141 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71H TYR* 3.4 12.7 + - + -
72H VAL* 5.6 7.0 - - + -
74H ASN* 2.7 42.6 + - + +
75H SER* 4.4 9.8 + - - +
139H ASP* 2.8 41.3 + - - +
140H PRO* 1.3 71.8 - - - +
142H VAL* 1.3 61.2 + - - +
143H GLU 3.3 1.1 - - - -
144H GLU* 3.2 13.5 + - - +
145H ALA* 3.1 20.3 + - - +
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 4.1 10.1 - - + -
72H VAL* 5.2 10.7 - - + +
83H PHE* 5.1 1.1 - - + -
134H ALA* 3.4 31.6 - - + -
136H VAL* 3.6 36.6 - - + -
140H PRO* 3.6 13.0 - - + -
141H ASN* 1.3 78.8 - - - +
143H GLU* 1.3 65.9 + - - +
144H GLU 3.0 1.8 - - - -
145H ALA* 3.0 20.0 + - + +
146H TRP* 3.0 36.9 + - + +
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Residues in contact with GLU 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 4.6 13.5 - - + +
140H PRO* 4.0 29.2 - - + +
142H VAL* 1.3 83.5 - - - +
144H GLU* 1.3 60.4 + - - +
146H TRP* 4.9 0.4 - - - -
147H ARG* 3.4 17.0 + - - +
159H ILE* 3.4 42.9 - - + +
161H SER* 5.0 7.6 - - - -
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Residues in contact with GLU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H TYR* 3.5 29.2 - - + +
140H PRO 5.5 0.9 - - - +
141H ASN* 3.2 14.6 + - - +
142H VAL 3.0 0.6 - - - -
143H GLU* 1.3 78.8 - - - +
145H ALA* 1.3 64.9 + - - +
146H TRP 3.0 2.9 + - - -
147H ARG* 3.1 53.9 + - - +
148H ARG* 3.3 19.4 + - - +
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Residues in contact with ALA 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ALA* 3.2 48.9 - - + +
71H TYR* 3.6 19.7 - - + -
72H VAL* 4.7 8.1 - - + +
83H PHE* 5.2 2.5 - - + -
141H ASN 3.1 9.2 + - - +
142H VAL* 3.0 15.4 + - + +
144H GLU* 1.3 76.6 - - - +
146H TRP* 1.3 62.2 + - + +
148H ARG* 3.7 4.1 - - - +
149H ALA 3.3 11.6 + - - -
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Residues in contact with TRP 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 2.6 62.8 - - + -
47H GLU* 3.0 22.2 - - - -
48H LEU* 3.8 20.6 - - + +
83H PHE* 2.8 46.0 - + - -
132H PHE* 3.9 15.6 - - + +
133H ILE 3.9 2.9 - - - -
134H ALA* 3.3 18.8 - - + -
142H VAL* 3.0 15.5 + - + +
144H GLU 3.0 0.8 - - - -
145H ALA* 1.3 82.2 - - + +
147H ARG* 1.3 65.6 + - - +
148H ARG 2.9 2.2 - - - -
149H ALA* 3.0 20.8 + - + +
150H LYS* 3.0 21.7 + - - +
159H ILE* 3.8 16.4 - - + -
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Residues in contact with ARG 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11350 G 4.2 17.3 - - - +
25020 C 3.0 17.9 + - - -
25030 A 2.5 30.7 + - - -
143H GLU 3.4 8.3 + - - +
144H GLU* 3.1 45.2 + - - +
146H TRP* 1.3 78.3 - - - +
148H ARG* 1.3 78.5 + - - +
150H LYS* 3.2 32.1 - - - +
151H MET* 3.6 21.9 - - - +
159H ILE* 4.0 1.5 - - + +
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Residues in contact with ARG 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25020 C 4.3 10.3 + - - +
25030 A 4.2 23.3 + - - -
25040 A 3.1 35.3 + - - -
67H ALA* 4.1 28.9 + - + +
70H ARG* 5.8 1.2 - - - +
71H TYR* 3.7 43.3 - - - +
144H GLU* 3.3 15.6 + - - +
145H ALA 3.7 8.5 - - - +
146H TRP 2.9 0.2 - - - -
147H ARG* 1.3 101.5 - - - +
149H ALA* 1.3 59.6 + - - +
151H MET* 2.9 22.1 - - - +
152H LYS* 4.0 9.0 + - - +
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Residues in contact with ALA 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LEU* 4.0 11.2 - - + -
64H ALA* 3.7 38.5 - - - +
68H ALA* 4.0 7.4 - - + -
132H PHE* 4.4 8.3 - - + -
145H ALA 3.3 14.5 + - - +
146H TRP* 3.0 16.8 + - + +
148H ARG* 1.3 75.0 - - - +
150H LYS* 1.3 58.0 + - - +
151H MET 2.8 10.5 + - - -
152H LYS* 3.0 12.3 + - - -
153H VAL* 3.8 3.9 + - - +
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Residues in contact with LYS 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11340 G 3.8 16.4 + - - +
11350 G 4.9 14.5 + - - -
48H LEU* 4.1 10.5 - - + +
146H TRP 3.0 25.8 + - - +
147H ARG* 3.2 36.5 - - - +
149H ALA* 1.3 75.1 - - - +
151H MET* 1.3 60.4 + - - +
152H LYS 3.3 0.7 - - - -
153H VAL* 3.6 13.8 - - - +
157H ILE* 3.4 48.2 - - + -
159H ILE* 3.6 18.4 - - - +
8309H NA 2.8 26.7 - - - -
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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