Contacts of the helix formed by residues 141 - 150 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B GLU* 2.7 39.1 + - - -
385B PRO* 4.0 6.7 - - - -
136C ILE* 3.7 22.2 - - + -
138C ASP* 2.9 14.6 + - + +
140C MET* 1.3 77.2 - - - +
142C PHE* 1.3 59.4 + - - +
143C PRO* 3.5 1.1 - - - -
144C ASP* 3.1 17.9 + - - +
145C MET* 2.9 27.5 + - - +
166C PHE* 4.0 6.9 - - + -
170C ARG* 4.3 18.2 - - - +
172C GLU* 5.0 0.7 - - - +
19D ASN* 3.1 25.9 + - - +
20D GLN* 2.8 42.0 + - - +
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Residues in contact with PHE 142 (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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55C VAL* 4.2 12.6 - - + -
56C HIS* 6.3 0.2 - - - -
97C VAL* 6.1 2.7 - - + -
134C PHE* 3.9 24.7 - + - -
136C ILE* 3.5 12.2 - - + +
139C ALA 3.0 12.7 + - - +
141C LYS* 1.3 77.3 - - - +
143C PRO* 1.4 61.8 - - + +
145C MET* 3.8 11.5 - - + +
146C VAL* 2.9 53.5 + - + +
501C HEM 3.2 83.2 - + + -
45D PHE* 3.5 24.5 - + - -
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Residues in contact with PRO 143 (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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139C ALA 3.7 8.5 - - - +
140C MET 3.8 7.4 - - - +
141C LYS 3.7 2.7 - - - -
142C PHE* 1.4 94.7 - - + +
144C ASP* 1.3 51.9 + - - +
146C VAL* 3.8 0.3 - - - +
147C HIS* 2.8 50.8 + - + -
41D LYS* 4.2 24.2 - - + +
42D ILE* 3.8 19.5 - - + -
45D PHE* 4.0 37.7 - - + -
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Residues in contact with ASP 144 (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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366B TYR* 4.0 13.0 - - - +
382B ASN 4.4 0.4 - - - +
383B TYR* 3.2 19.3 - - - +
384B GLU* 3.1 43.8 + - - +
140C MET 3.7 1.9 - - - +
141C LYS* 3.1 21.6 + - - +
143C PRO* 1.3 76.2 - - - +
145C MET* 1.3 63.1 + - - +
147C HIS* 3.3 1.7 + - - -
148C SER* 3.0 19.6 + - - -
166C PHE* 3.6 8.3 - - + -
19D ASN* 3.8 1.0 + - - -
41D LYS* 2.7 32.1 + - - -
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Residues in contact with MET 145 (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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97C VAL* 6.0 4.9 - - + -
98C ILE* 5.8 1.3 - - + -
134C PHE* 3.7 32.8 - - + -
135C PHE* 3.6 29.8 - - + -
136C ILE* 4.2 9.9 - - + -
141C LYS 2.9 16.1 + - - +
142C PHE* 3.4 18.8 + - + +
144C ASP* 1.3 75.3 - - - +
146C VAL* 1.3 72.7 + - + +
148C SER* 3.0 18.3 + - - -
149C LEU* 3.2 28.7 + - + +
166C PHE* 3.6 30.4 - - + -
167C MET* 3.8 14.8 - - + -
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Residues in contact with VAL 146 (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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54C VAL 5.1 0.2 - - - +
55C VAL* 3.8 20.9 - - + -
97C VAL* 6.2 0.7 - - + -
98C ILE* 4.9 5.2 - - + -
142C PHE* 2.9 57.8 + - + +
143C PRO 3.8 2.7 - - - +
145C MET* 1.3 82.2 - - + +
147C HIS* 1.3 56.5 + - + +
149C LEU* 3.1 6.4 + - - +
150C LYS* 2.8 56.8 + - + +
45D PHE* 3.6 21.3 - - + -
49D ARG* 5.1 0.4 - - - +
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Residues in contact with HIS 147 (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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366B TYR* 3.3 19.3 + - - +
367B GLN* 4.5 2.0 - - - -
368B ARG* 4.3 15.5 - - + +
382B ASN* 2.8 52.5 + - - +
383B TYR* 4.4 0.2 - - - -
143C PRO* 2.8 33.8 + - + +
144C ASP* 3.7 4.2 + - - +
146C VAL* 1.3 77.0 - - + +
148C SER* 1.3 58.5 + - - +
150C LYS* 3.7 14.7 + - + +
151C PRO 5.0 0.2 - - - +
162C ARG* 2.9 20.1 + - - -
45D PHE* 4.3 8.5 - + - -
48D GLU* 2.6 38.3 + - - -
49D ARG* 6.2 0.2 - - - -
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Residues in contact with SER 148 (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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383B TYR* 3.8 15.0 - - - +
144C ASP 3.0 11.4 + - - -
145C MET 3.0 12.3 + - - -
146C VAL 3.1 0.6 - - - -
147C HIS* 1.3 76.5 - - - +
149C LEU* 1.3 60.8 + - - +
150C LYS 3.8 0.5 - - - +
159C ASP 4.5 1.2 + - - +
162C ARG* 3.2 21.1 + - - +
163C TYR* 3.3 37.4 + - - +
166C PHE* 3.4 34.3 - - - +
167C MET* 4.8 1.0 - - - +
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Residues in contact with LEU 149 (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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98C ILE* 3.4 31.8 - - + +
109C ASP* 5.9 1.3 - - - +
135C PHE* 4.6 13.0 - - + -
145C MET* 3.2 41.0 + - + +
146C VAL 3.1 1.0 + - - +
148C SER* 1.3 78.6 + - - +
150C LYS* 1.3 64.5 + - - +
158C GLN* 2.8 35.7 + - - +
163C TYR* 3.8 33.9 - - + -
167C MET* 3.8 24.5 - - + -
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Residues in contact with LYS 150 (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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382B ASN* 6.1 1.1 - - - +
52C GLU* 5.1 5.3 + - - -
53C ARG 5.2 0.4 + - - -
54C VAL 3.1 15.4 + - - -
55C VAL* 4.3 5.5 - - - +
57C ALA* 6.3 1.0 - - - +
97C VAL 4.7 1.0 + - - -
98C ILE* 2.6 36.5 + - + +
99C HIS 5.1 2.2 + - - -
146C VAL* 2.8 44.3 + - + +
147C HIS* 4.0 13.9 - - + +
148C SER 3.4 0.9 - - - +
149C LEU* 1.3 75.9 - - - +
151C PRO* 1.3 83.2 - - + +
152C ASP 3.2 2.3 + - - -
158C GLN* 4.5 2.5 - - - +
159C ASP 5.0 0.7 + - - -
162C ARG* 3.4 14.4 + - - -
49D ARG* 3.0 34.7 - - - +
102D HIS* 5.6 4.1 - - + -
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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