Contacts of the helix formed by residues 35 - 46 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ARG* 2.7 37.0 + - - +
22B SER* 3.4 7.4 - - - -
23B ARG* 2.7 40.7 + - + +
32B LEU* 3.0 16.7 + - - +
33B LEU 3.2 1.0 - - - -
34B GLU* 1.3 76.0 - - - +
36B TYR* 1.3 61.1 + - - +
37B GLN 3.4 0.5 + - - -
38B LEU* 3.0 32.6 + - + +
39B ILE* 3.1 26.1 + - + +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 5.2 0.6 - - - +
10B THR* 4.5 10.8 - - + -
12B GLN* 2.9 36.9 + - + -
33B LEU 5.4 0.2 - - - -
34B GLU 2.7 13.0 + - - +
35B ASP* 1.3 71.4 + - - +
37B GLN* 1.3 60.5 + - - +
39B ILE* 3.9 7.1 - - + +
40B GLU* 2.7 69.9 + - + +
316D ASN* 4.4 10.1 - - - -
318D GLY* 4.3 19.7 - - - +
319D VAL* 3.9 10.8 - - + -
336D LEU* 4.9 6.1 - - + -
340D SER* 3.6 26.6 + - - -
344D ARG* 5.0 3.0 + - - -
351D TYR* 4.4 4.2 + - - -
352D GLN* 5.2 0.3 - - - +
400D GLU* 5.9 0.2 + - - -
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MET* 3.3 25.9 - - + +
412A ARG* 3.8 18.6 + - - +
10B THR* 4.6 12.5 - - + +
16B ILE* 3.5 46.3 - - + +
17B GLY 4.8 1.2 + - - -
18B ASP 2.8 27.8 + - - +
19B ASN* 3.9 4.0 + - - +
35B ASP* 3.2 6.2 + - - +
36B TYR* 1.3 84.6 - - - +
38B LEU* 1.3 62.0 + - - +
40B GLU* 4.0 3.1 - - - +
41B LYS* 3.2 25.3 + - + +
367D GLN* 5.6 0.2 + - - -
400D GLU* 4.2 11.5 + - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ALA* 3.9 9.2 - - + -
140A MET* 3.6 48.4 - - + +
334A GLY* 5.0 3.6 - - - -
22B SER* 3.7 17.9 - - - +
31B THR* 3.9 22.9 - - + -
35B ASP* 3.0 29.1 + - + +
37B GLN* 1.3 76.9 - - - +
39B ILE* 1.3 61.7 + - + +
41B LYS* 3.2 4.2 + - + +
42B ILE* 2.8 47.4 + - + +
33C LEU* 4.4 13.0 - - + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 4.1 27.5 - - + -
32B LEU 4.7 1.6 - - - +
33B LEU* 3.2 38.1 - - + +
35B ASP* 3.1 16.4 + - + +
36B TYR* 4.0 6.7 - - + +
38B LEU* 1.3 80.6 - - + +
40B GLU* 1.3 58.8 + - - +
42B ILE* 4.5 1.6 - - - +
43B ALA* 2.7 39.4 + - - +
33C LEU* 4.1 24.9 - - + -
337D PHE* 4.7 16.2 - - + -
340D SER* 6.3 0.7 - - - -
344D ARG* 4.4 15.7 - - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.4 9.0 - - - +
11B ASN* 2.6 55.1 + - + +
12B GLN 3.9 1.9 + - - -
36B TYR* 2.7 60.7 + - + +
37B GLN* 4.0 3.6 - - - +
39B ILE* 1.3 76.4 - - - +
41B LYS* 1.3 61.7 + - - +
43B ALA* 4.0 0.7 - - - +
44B HIS* 3.1 24.4 + - - +
344D ARG* 3.7 16.4 + - - +
352D GLN* 5.1 0.3 - - - +
367D GLN* 3.1 14.9 + - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MET* 2.8 35.6 + - - +
143A PRO* 4.2 20.8 - - + +
144A ASP* 2.7 34.7 + - - -
16B ILE* 6.5 0.2 - - + -
19B ASN* 2.9 30.2 + - - +
37B GLN* 3.2 17.2 + - + +
38B LEU* 3.4 5.4 - - + +
40B GLU* 1.3 76.9 - - - +
42B ILE* 1.3 65.4 + - + +
44B HIS* 3.4 2.6 + - - +
45B PHE* 3.1 23.3 + - - +
366D TYR* 5.9 4.7 - - - -
367D GLN* 3.9 25.8 - - + +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 3.5 24.5 - - + +
140A MET* 5.5 0.2 - - - -
143A PRO* 3.8 20.4 - - + -
334A GLY* 4.9 2.7 - - - +
337A PHE* 4.0 15.7 - - + -
338A SER* 3.6 22.2 - - - +
501A HEM 3.9 20.4 - - + -
38B LEU* 2.8 40.1 + - + +
39B ILE* 4.3 1.6 - - - +
41B LYS* 1.3 74.6 - - + +
43B ALA* 1.3 59.2 + - - +
45B PHE* 3.3 6.5 + - + +
46B ASP* 2.8 49.8 + - - +
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Residues in contact with ALA 43 (chain B).
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* 4.0 9.4 - - + -
341A ASP* 3.6 17.9 - - - +
39B ILE 2.7 25.7 + - - +
40B GLU 4.2 0.2 - - - +
42B ILE* 1.3 74.4 - - - +
44B HIS* 1.3 59.4 + - - +
46B ASP 3.6 4.0 + - - -
47B ARG* 2.7 31.9 + - - +
344D ARG* 3.5 35.0 - - - +
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 4.7 5.6 - - - +
40B GLU* 3.1 15.4 + - + +
41B LYS 4.0 2.9 - - - +
42B ILE 3.2 0.2 - - - -
43B ALA* 1.3 74.1 - - - +
45B PHE* 1.3 65.8 + - - +
46B ASP 3.1 1.1 - - - -
47B ARG* 3.0 15.6 + - - +
48B GLU* 3.2 10.3 + - - +
344D ARG* 5.1 2.2 - - - +
349D PRO* 3.8 20.2 - - + -
350D ASN* 2.6 28.4 + - - -
353D GLN* 5.4 1.0 + - - -
367D GLN* 3.4 30.9 + - + +
368D ARG* 3.2 40.1 + - - -
369D ASP 3.3 14.0 + - - -
370D GLY* 4.5 2.7 - - - -
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.5 51.8 - - + +
55A VAL* 4.5 2.0 - - + -
142A PHE* 3.5 38.6 - + - -
143A PRO* 3.9 29.6 - - + -
146A VAL* 3.7 29.4 - - + -
147A HIS* 4.1 4.0 - + - -
338A SER* 5.0 0.9 - - - -
501A HEM 4.2 5.8 - - + -
41B LYS 3.1 13.9 + - - +
42B ILE* 3.4 10.5 - - + +
44B HIS* 1.3 78.2 + - - +
46B ASP* 1.3 71.4 + - - +
47B ARG 3.1 1.0 + - - -
48B GLU* 3.5 33.6 + - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.0 4.0 - - - +
338A SER* 2.7 39.5 + - - +
341A ASP* 2.4 34.6 - - - +
342A THR* 2.6 34.5 + - - -
345A HIS* 3.3 12.0 + - - -
501A HEM 3.5 9.7 - - - +
42B ILE* 2.8 39.2 + - - +
43B ALA 3.7 4.0 - - - +
44B HIS 3.1 0.4 - - - -
45B PHE* 1.3 75.9 - - - +
47B ARG* 1.3 59.1 + - - +
48B GLU 4.2 0.2 + - - -
49B ARG 5.4 0.2 + - - -
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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