Contacts of the helix formed by residues 141 - 150 (chain D) in PDB entry 2J2M
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 LYS 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A GLU* 2.8 30.0 + - - -
385A PRO* 3.9 7.0 - - - -
19C ASN* 3.2 30.6 + - - +
20C GLN* 2.9 40.0 + - - +
136D ILE* 3.7 21.5 - - + -
138D ASP* 3.0 15.3 + - + +
139D ALA 2.9 0.4 + - - -
140D MET* 1.3 75.7 - - - +
142D PHE* 1.3 59.8 + - - +
143D PRO* 3.5 2.2 - - - -
144D ASP* 3.2 17.2 + - - +
145D MET* 2.8 27.0 + - - +
166D PHE* 4.0 9.3 - - + -
170D ARG* 4.0 22.7 - - + +
172D GLU* 5.0 0.7 - - - +
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Residues in contact with PHE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ILE* 4.7 0.2 - - + -
45C PHE* 3.6 21.5 - + - -
55D VAL* 4.2 12.1 - - + -
56D HIS* 6.3 0.2 - - - -
97D VAL* 6.1 2.5 - - + -
134D PHE* 3.8 12.8 - + - -
136D ILE* 3.6 10.1 - - + +
139D ALA 2.9 15.4 + - - +
141D LYS* 1.3 77.5 - - - +
143D PRO* 1.3 64.7 - - + +
145D MET* 3.2 26.3 + - + +
146D VAL* 3.0 48.5 + - + +
501D HEM 3.3 83.0 - + + -
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Residues in contact with PRO 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.8 29.4 - - + +
42C ILE* 4.0 11.9 - - + -
45C PHE* 3.9 40.8 - - + -
139D ALA 3.8 7.0 - - - +
140D MET 3.9 8.3 - - - +
141D LYS 3.6 3.6 - - - -
142D PHE* 1.3 92.5 - - + +
144D ASP* 1.3 56.7 + - - +
146D VAL 3.8 0.2 - - - -
147D HIS* 2.8 47.3 + - + +
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Residues in contact with ASP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 3.9 13.7 - - - +
382A ASN 4.8 0.7 - - - -
383A TYR* 3.4 18.4 - - - +
384A GLU* 3.1 45.1 + - - +
19C ASN* 4.4 0.8 + - - -
41C LYS* 2.5 35.1 + - - -
140D MET 3.7 2.1 - - - +
141D LYS* 3.2 20.0 + - - +
143D PRO* 1.3 75.7 - - - +
145D MET* 1.3 63.6 + - - +
147D HIS* 4.5 1.3 + - - -
148D SER* 3.1 21.5 + - - -
166D PHE* 3.7 8.4 - - + -
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 5.7 1.3 - - + -
134D PHE* 3.5 39.9 - - + -
135D PHE* 3.6 25.1 - - + -
136D ILE* 4.1 10.3 - - + -
141D LYS 2.8 19.7 + - - +
142D PHE* 3.2 19.5 + - + +
144D ASP* 1.3 74.1 - - - +
146D VAL* 1.3 70.8 + - + +
148D SER* 3.1 18.0 + - - -
149D LEU* 3.3 27.3 + - + +
166D PHE* 3.7 30.2 - - + -
167D MET* 3.9 13.9 - - + -
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 3.7 19.1 - - + -
49C ARG* 5.1 0.9 - - - +
54D VAL 5.0 0.2 - - - +
55D VAL* 3.7 23.6 - - + -
98D ILE* 4.8 3.8 - - + -
142D PHE* 3.0 57.3 + - + +
143D PRO 3.8 2.9 - - - +
145D MET* 1.3 82.1 - - + +
147D HIS* 1.3 55.8 + - + +
149D LEU* 3.0 8.1 + - - +
150D LYS* 2.7 57.9 + - + +
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Residues in contact with HIS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 3.1 19.7 + - - +
367A GLN* 4.5 1.6 - - - -
368A ARG* 4.2 17.0 - - + +
382A ASN* 2.8 51.3 + - - +
45C PHE* 4.2 9.5 - + - -
48C GLU* 2.5 38.1 + - - -
143D PRO* 2.8 34.9 + - + +
144D ASP* 3.8 3.1 + - - +
146D VAL* 1.3 76.7 - - + +
148D SER* 1.3 59.8 + - - +
150D LYS* 3.5 16.8 + - + +
151D PRO 4.7 0.5 - - - +
162D ARG* 3.0 18.2 + - - -
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A TYR* 3.8 15.8 - - - +
144D ASP 3.1 14.7 + - - -
145D MET 3.1 10.2 + - - -
147D HIS* 1.3 76.7 - - - +
149D LEU* 1.3 62.2 + - - +
150D LYS 3.8 1.0 - - - +
159D ASP 4.5 1.0 + - - +
162D ARG* 3.3 24.0 + - - +
163D TYR* 3.4 37.5 + - - +
166D PHE* 3.5 28.8 - - - +
167D MET* 4.6 0.5 - - - +
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 6.2 0.2 - - + -
98D ILE* 3.4 30.6 - - + +
109D ASP* 6.1 0.4 - - - +
135D PHE* 4.8 14.1 - - + -
145D MET* 3.3 39.4 + - + +
146D VAL 3.0 3.9 + - - +
148D SER* 1.3 77.7 + - - +
150D LYS* 1.3 64.1 + - - +
158D GLN* 2.9 37.9 + - - +
163D TYR* 3.7 33.7 - - + -
167D MET* 3.8 22.9 - - + -
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ASN* 6.3 0.4 - - - +
49C ARG* 3.1 28.3 - - - +
102C HIS* 5.7 3.3 - - + -
52D GLU* 5.2 4.4 + - - -
53D ARG 5.1 1.2 + - - -
54D VAL 3.0 21.9 + - - -
55D VAL* 4.0 8.4 - - - +
57D ALA* 6.0 1.2 - - - +
97D VAL 4.6 0.2 + - - -
98D ILE* 2.6 35.3 + - + +
99D HIS* 4.8 3.8 - - - +
146D VAL* 2.7 40.6 + - + +
147D HIS* 3.5 13.2 + - + +
148D SER 3.8 0.9 - - - +
149D LEU* 1.3 78.5 - - - +
151D PRO* 1.3 82.3 - - + +
152D ASP 3.3 1.9 + - - -
158D GLN* 4.5 3.1 - - - +
159D ASP 5.1 0.7 + - - -
162D ARG* 3.5 12.8 + - - -
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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