Contacts of the helix formed by residues 42 - 55 (chain M) in PDB entry 2J28
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 THR 42 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2485B G 4.2 5.8 - - - +
40M ARG* 3.3 4.4 + - + -
41M LEU* 1.3 76.1 - - - +
43M ALA* 1.3 70.6 + - - +
44M ARG* 3.3 15.0 + - + +
45M GLN* 2.7 52.0 + - + +
46M ILE* 2.8 11.8 + - - +
90M GLU* 4.3 4.5 + - - +
91M TYR* 2.9 40.6 + - - -
92M TRP* 3.7 10.5 - - - +
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Residues in contact with ALA 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M GLN* 3.5 12.1 - - - +
4M PRO* 3.7 14.6 - - + -
5M LYS 4.9 0.4 - - - +
41M LEU 3.7 1.4 + - - -
42M THR* 1.3 74.9 + - - +
44M ARG* 1.3 56.0 + - - +
46M ILE* 3.2 3.9 + - - +
47M GLU* 2.6 47.6 + - - +
69M PRO* 4.3 11.2 - - + +
71M LYS* 4.3 6.7 - - - -
91M TYR* 3.2 31.0 - - + +
92M TRP 4.3 0.6 - - - +
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Residues in contact with ARG 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2484B G 3.5 40.4 + - - +
2485B G 5.7 2.6 + - - +
1M MET* 5.8 0.4 - - - -
3M GLN* 4.1 9.0 - - - +
42M THR* 3.1 15.8 + - + +
43M ALA* 1.3 78.9 - - - +
45M GLN* 1.3 62.4 + - - +
47M GLU* 3.1 9.3 + - - +
48M ALA* 3.0 25.5 + - - +
89M VAL* 5.1 3.0 + - - +
90M GLU* 3.9 27.1 + - - +
91M TYR* 3.3 35.0 + - + +
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Residues in contact with GLN 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2484B G 3.9 6.9 + - - +
2485B G 3.4 34.7 + - - +
2486B C 5.6 0.8 + - - -
40M ARG* 2.7 32.9 + - - +
41M LEU* 3.7 12.1 - - + +
42M THR* 2.7 37.7 + - + +
44M ARG* 1.3 73.7 - - - +
46M ILE* 1.3 63.3 + - + +
48M ALA* 3.2 6.2 + - - +
49M ALA* 3.0 24.6 + - - +
119M LEU* 4.0 7.9 - - - +
120M ALA* 5.3 2.0 - - - -
121M ALA* 3.2 31.4 + - - +
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Residues in contact with ILE 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M PRO* 3.8 23.1 - - + -
41M LEU* 3.4 52.0 - - + +
42M THR 2.8 9.3 + - - +
43M ALA* 3.6 7.0 - - - +
45M GLN* 1.3 74.6 - - - +
47M GLU* 1.3 61.3 + - - +
49M ALA* 3.4 3.8 + - + +
50M ARG* 3.1 55.9 + - + +
65M ILE* 4.4 11.7 - - + -
67M VAL* 3.6 20.9 - - + -
69M PRO* 5.2 0.9 - - + -
93M VAL* 4.3 2.0 - - + -
100M LYS* 5.8 2.5 - - + +
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Residues in contact with GLU 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2484B G 4.7 0.3 + - - -
1M MET* 3.6 13.1 - - + +
2M LEU* 2.5 57.0 - - + +
3M GLN* 2.7 23.0 + - - -
4M PRO* 2.9 24.5 - - + +
43M ALA 2.6 35.4 + - - +
44M ARG* 3.7 8.2 - - - +
46M ILE* 1.3 70.5 - - - +
48M ALA* 1.3 61.3 + - - +
50M ARG* 4.8 2.2 - - - -
51M ARG* 2.7 39.4 + - - +
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Residues in contact with ALA 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2483B C 3.5 23.7 + - - +
2484B G 3.4 33.4 - - - +
44M ARG 3.0 18.6 + - - +
45M GLN 3.4 4.9 - - - +
47M GLU* 1.3 76.5 - - - +
49M ALA* 1.3 62.3 + - - +
51M ARG* 4.0 3.6 - - - +
52M ALA* 3.1 25.1 + - - +
119M LEU* 3.7 10.2 - - + +
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Residues in contact with ALA 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M GLN 3.0 15.6 + - - +
46M ILE* 3.7 7.4 - - + +
48M ALA* 1.3 75.8 - - - +
50M ARG* 1.3 82.4 + - - +
52M ALA* 2.9 18.4 + - - +
53M MET* 3.5 9.2 + - - +
116M ALA* 3.9 14.1 - - - +
119M LEU* 3.6 19.9 - - + +
120M ALA* 4.7 12.1 - - + +
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Residues in contact with ARG 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M LEU* 6.3 0.4 - - + -
33M LEU* 4.4 7.7 - - - +
46M ILE* 3.1 51.9 + - + +
47M GLU* 4.1 2.7 - - - +
49M ALA* 1.3 85.4 - - - +
51M ARG* 1.3 58.4 + - - +
53M MET* 2.8 67.0 + - + +
54M THR* 4.3 1.4 + - - +
63M ILE* 4.2 9.3 - - + +
64M TRP 3.7 18.3 + - - -
65M ILE* 4.3 15.4 - - + +
67M VAL* 5.7 0.4 - - - +
100M LYS* 3.3 21.4 + - - +
101M VAL* 3.0 29.5 - - - +
124M LEU* 5.8 0.4 - - - +
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Residues in contact with ARG 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2483B C 4.9 13.0 - - - -
1M MET* 5.0 5.9 - - - +
2M LEU* 3.7 41.8 - - + +
47M GLU 2.7 23.8 + - - +
48M ALA 4.0 1.8 - - - +
50M ARG* 1.3 73.8 - - - +
52M ALA* 1.3 60.0 + - - +
53M MET 3.2 0.9 + - - -
54M THR* 3.7 21.7 + - - +
55M ARG* 4.1 3.4 + - - +
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2483B C 5.2 4.0 - - - +
48M ALA 3.1 19.1 + - - +
49M ALA 2.9 8.3 + - - +
51M ARG* 1.3 75.3 - - - +
53M MET* 1.3 59.6 + - - +
55M ARG* 2.8 49.1 - - - +
112M LEU* 4.3 1.6 - - - +
115M GLU 5.3 0.2 - - - -
116M ALA* 3.7 19.1 - - + +
119M LEU* 4.1 12.8 - - + -
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Residues in contact with MET 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M ALA 3.5 10.3 - - - +
50M ARG* 2.8 60.1 + - - +
52M ALA* 1.3 75.8 - - - +
54M THR* 1.3 70.0 + - - +
55M ARG* 3.9 0.3 - - - +
57M VAL* 3.5 2.9 - - - +
63M ILE* 3.4 37.9 - - + -
64M TRP 4.7 0.9 - - - +
101M VAL* 4.7 8.7 - - + +
103M TYR* 3.2 35.2 - - + +
112M LEU* 2.8 35.6 - - + +
113M ALA* 5.7 4.9 - - - -
116M ALA* 4.3 5.8 - - + -
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Residues in contact with THR 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M ARG 5.1 1.1 - - - +
51M ARG* 3.7 14.7 + - - +
53M MET* 1.3 73.6 - - - +
55M ARG* 1.3 64.8 + - - +
56M ALA 3.3 2.6 + - - -
57M VAL* 2.4 40.8 + - - +
58M LYS 4.4 18.8 - - - +
59M ARG* 5.7 9.0 - - + -
63M ILE* 4.7 17.3 - - + -
112M LEU* 4.8 1.8 - - - -
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Residues in contact with ARG 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2467B C 5.2 2.4 + - - -
2468B A 3.0 43.9 + - - -
2469B A 3.1 44.8 + - - +
2482B A 3.4 30.5 + - - +
2483B C 5.6 0.4 + - - -
51M ARG* 4.1 3.5 + - - +
52M ALA* 2.8 47.4 + - - +
53M MET 3.9 1.6 - - - +
54M THR* 1.3 87.5 + - - +
56M ALA* 1.3 64.9 + - - +
57M VAL* 2.8 9.1 + - + +
112M LEU* 5.8 0.4 - - + -
115M GLU* 4.5 20.6 + - - -
119M LEU* 5.9 1.4 - - - +
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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