Contacts of the helix formed by residues 35 - 46 (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 ASP 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C SER* 3.4 4.9 - - - -
23C ARG* 2.7 41.8 + - + +
31C THR* 4.8 0.2 - - + -
32C LEU* 2.9 18.2 + - - +
33C LEU 3.2 3.0 - - - -
34C GLU* 1.3 74.9 - - - +
36C TYR* 1.3 55.5 + - - +
37C GLN 3.7 0.2 + - - -
38C LEU* 3.1 35.7 + - + +
39C ILE* 3.0 30.8 + - - +
412D ARG* 2.7 37.2 + - - +
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Residues in contact with TYR 36 (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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316A ASN* 4.5 7.0 - - - -
318A GLY 4.2 22.4 - - - +
319A VAL* 3.8 11.9 - - + -
336A LEU* 5.0 6.1 - - + -
340A SER* 3.7 24.6 + - - -
344A ARG* 4.8 2.9 + - - -
351A TYR* 4.6 2.8 + - - -
352A GLN* 5.2 0.7 - - - +
400A GLU* 5.9 0.4 + - - -
10C THR* 4.4 10.8 - - + -
12C GLN* 3.0 35.7 + - + -
33C LEU 5.3 0.9 - - - -
34C GLU 2.7 13.4 + - - +
35C ASP* 1.3 69.2 + - - +
37C GLN* 1.3 60.8 + - - +
39C ILE* 4.5 5.6 - - + +
40C GLU* 2.7 74.6 + - + +
412D ARG* 5.2 0.6 - - - +
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Residues in contact with GLN 37 (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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400A GLU* 4.1 11.2 + - - +
10C THR* 4.4 12.9 - - + +
16C ILE* 3.7 44.0 - - + +
17C GLY 4.9 1.2 + - - -
18C ASP 2.9 27.7 + - - +
19C ASN* 4.1 3.6 + - - +
36C TYR* 1.3 86.1 - - - +
38C LEU* 1.3 61.4 + - - +
40C GLU* 4.0 3.6 - - - +
41C LYS* 3.1 28.9 + - + +
140D MET* 3.4 25.1 - - + +
412D ARG* 3.7 25.2 + - - +
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Residues in contact with LEU 38 (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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33B LEU* 4.1 15.9 - - + -
22C SER* 3.8 11.9 - - - +
31C THR* 3.7 29.8 - - + -
35C ASP* 3.1 30.9 + - + +
37C GLN* 1.3 76.4 - - - +
39C ILE* 1.3 63.2 + - + +
41C LYS* 3.4 2.1 + - + +
42C ILE* 2.9 52.3 + - + +
139D ALA* 4.1 4.9 - - + -
140D MET* 3.6 45.3 - - + +
334D GLY* 5.2 6.1 - - - -
337D PHE* 6.6 0.7 - - + -
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Residues in contact with ILE 39 (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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337A PHE* 4.5 15.7 - - + -
344A ARG* 4.3 15.0 - - - +
33B LEU* 3.9 18.6 - - + -
32C LEU 4.8 1.6 - - - +
33C LEU* 3.2 48.2 - - + +
35C ASP 3.0 17.1 + - - +
36C TYR* 4.1 6.1 - - + +
38C LEU* 1.3 83.9 - - + +
40C GLU* 1.3 60.4 + - - +
42C ILE* 4.2 0.8 - - - +
43C ALA* 2.8 34.8 + - - +
337D PHE* 3.9 30.0 - - + -
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Residues in contact with GLU 40 (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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344A ARG* 3.8 18.3 + - - +
352A GLN* 5.1 0.3 - - - +
367A GLN* 3.1 15.6 + - - +
10C THR* 3.5 10.5 - - - +
11C ASN* 2.9 54.8 + - + +
12C GLN 3.9 1.4 + - - -
36C TYR* 2.7 62.8 + - + +
37C GLN 4.0 3.7 - - - +
39C ILE* 1.3 72.4 - - - +
41C LYS* 1.3 56.0 + - - +
43C ALA* 3.8 0.9 - - - +
44C HIS* 2.9 30.9 + - + +
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Residues in contact with LYS 41 (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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366A TYR* 6.0 2.9 - - - -
367A GLN* 3.7 26.4 - - + +
16C ILE* 6.3 2.0 - - + -
19C ASN* 2.9 29.4 + - - +
37C GLN* 3.1 19.2 + - + +
38C LEU 3.7 3.4 - - - +
39C ILE 3.3 0.2 - - - -
40C GLU* 1.3 79.5 - - - +
42C ILE* 1.3 60.0 + - + +
44C HIS* 3.5 2.4 + - - +
45C PHE* 3.0 28.2 + - - +
140D MET* 2.9 32.3 + - - +
143D PRO* 3.8 24.8 - - + +
144D ASP* 2.5 36.1 + - - -
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Residues in contact with ILE 42 (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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38C LEU* 2.9 38.0 + - + +
39C ILE 4.2 1.3 - - - +
41C LYS* 1.3 73.5 - - + +
43C ALA* 1.3 55.9 + - - +
45C PHE* 3.2 7.5 + - + +
46C ASP* 2.6 53.7 + - - +
139D ALA* 3.6 25.6 - - + +
140D MET* 5.2 0.7 - - - -
142D PHE* 5.5 0.4 - - + -
143D PRO* 4.0 17.3 - - + -
334D GLY* 4.9 2.7 - - - +
337D PHE* 3.7 22.0 - - + -
338D SER* 3.7 16.6 - - - +
501D HEM 4.0 20.6 - - + -
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Residues in contact with ALA 43 (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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344A ARG* 3.6 29.4 - - - +
39C ILE 2.8 24.3 + - - +
40C GLU 4.0 0.7 - - - +
42C ILE* 1.3 74.2 - - - +
44C HIS* 1.3 61.4 + - - +
46C ASP* 3.2 9.4 + - - +
47C ARG* 3.1 38.6 + - - +
337D PHE* 4.2 7.4 - - + -
341D ASP* 3.5 15.3 - - - +
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Residues in contact with HIS 44 (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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344A ARG* 5.2 1.7 - - - +
349A PRO* 3.6 20.4 - - + -
350A ASN* 2.7 28.1 + - - -
353A GLN* 5.3 1.0 + - - -
367A GLN* 3.4 30.9 + - + +
368A ARG 2.9 45.0 + - - -
369A ASP 3.6 8.6 + - - -
370A GLY* 4.4 4.4 - - - -
11C ASN* 4.6 6.7 - - - +
40C GLU* 2.9 15.9 + - + +
41C LYS 3.9 2.5 - - - +
43C ALA* 1.3 71.9 - - - +
45C PHE* 1.3 58.9 + - - +
47C ARG* 2.8 26.7 + - - +
48C GLU* 3.2 10.0 + - - +
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Residues in contact with PHE 45 (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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367A GLN* 5.8 0.2 - - - +
41C LYS 3.0 15.0 + - - +
42C ILE* 3.3 11.0 - - + +
44C HIS* 1.3 75.4 + - - +
46C ASP* 1.3 69.1 + - - +
47C ARG 3.1 4.9 + - - -
48C GLU* 3.3 38.4 + - - +
54D VAL* 3.5 49.1 - - + +
55D VAL* 4.5 2.5 - - + -
142D PHE* 3.6 38.6 - + - -
143D PRO* 3.9 27.8 - - + -
146D VAL* 3.7 31.9 - - + -
147D HIS* 4.2 2.7 - + - -
338D SER* 5.0 1.8 - - - -
501D HEM 4.2 8.1 - - + -
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Residues in contact with ASP 46 (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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42C ILE* 2.6 27.3 + - - +
43C ALA 3.3 6.7 - - - +
44C HIS 3.1 0.4 - - - -
45C PHE* 1.3 78.7 - - - +
47C ARG* 1.3 58.8 + - - +
48C GLU 3.6 0.4 - - - -
54D VAL* 4.9 5.0 - - - +
338D SER* 2.9 44.5 + - - +
341D ASP* 2.6 31.3 - - - +
342D THR* 2.6 34.1 + - - -
345D HIS* 3.6 10.4 - - - -
501D HEM 3.3 11.6 - - - +
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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