Contacts of the helix formed by residues 44 - 58 (chain B) in PDB entry 3SJ5
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET 4.7 1.3 - - - +
42B ASP* 4.1 7.6 + - - +
43B ILE* 1.3 82.8 - - - +
45B ASP* 1.3 77.3 + - - +
46B ASP* 3.3 25.3 + - - +
47B GLU* 3.8 17.5 + - - +
48B VAL* 3.0 22.5 + - - +
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Residues in contact with ASP 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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1B MET* 3.6 33.9 + - - +
44B ASP* 1.3 84.6 + - - +
46B ASP* 1.3 63.0 + - - +
48B VAL* 3.3 8.2 + - - +
49B ARG* 3.1 44.4 + - - +
135B ARG* 3.4 31.1 + - - +
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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
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44B ASP* 3.3 15.1 + - - +
45B ASP* 1.3 77.2 - - - +
47B GLU* 1.3 65.9 + - - +
49B ARG* 3.3 21.0 + - - +
50B ARG* 3.1 40.8 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.5 22.9 - - + +
30B GLY* 5.3 0.2 - - - -
31B TRP* 3.2 42.0 + - + +
43B ILE* 5.1 2.4 - - + +
44B ASP* 3.8 19.8 + - + +
45B ASP 3.4 0.2 - - - -
46B ASP* 1.3 75.7 + - - +
48B VAL* 1.3 61.7 + - - +
50B ARG* 2.9 30.6 + - - +
51B ILE* 2.9 34.0 + - - +
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Residues in contact with VAL 48 (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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1B MET* 5.7 3.4 - - + -
6B VAL* 4.2 20.9 - - + -
9B TRP* 4.2 17.3 - - + -
43B ILE* 3.9 16.6 - - + +
44B ASP 3.0 24.9 - - - +
45B ASP* 3.3 12.1 + - - +
46B ASP 3.3 0.2 - - - -
47B GLU* 1.3 77.0 - - - +
49B ARG* 1.3 62.7 + - + +
51B ILE* 3.1 13.8 + - + +
52B PHE* 3.1 30.3 + - + -
67B TRP* 4.2 23.1 - - + -
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Residues in contact with ARG 49 (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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45B ASP* 3.1 47.0 + - - +
46B ASP* 3.4 22.4 + - - +
48B VAL* 1.3 77.9 - - + +
50B ARG* 1.3 57.4 + - + +
52B PHE* 3.4 5.7 + - - +
53B ALA* 2.9 29.9 + - - +
63B VAL* 5.6 0.3 - - - +
67B TRP* 5.8 7.6 - - + +
134B LYS 5.1 2.2 + - - -
135B ARG* 3.9 29.1 + - - +
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Residues in contact with ARG 50 (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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29B VAL* 3.8 32.6 + - + +
46B ASP* 3.1 32.2 + - - +
47B GLU* 2.9 36.9 + - - +
49B ARG* 1.3 74.7 - - + +
51B ILE* 1.3 66.3 + - - +
53B ALA* 3.5 7.9 + - + +
54B LYS* 3.1 24.9 + - - +
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Residues in contact with ILE 51 (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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6B VAL* 5.4 1.8 - - + -
10B ILE* 4.8 9.6 - - + -
13B LEU* 4.5 19.5 - - + -
22B VAL* 6.0 2.5 - - + -
25B SER* 4.2 8.5 - - - +
26B LEU* 3.9 26.5 - - + -
29B VAL* 3.9 22.9 - - + -
31B TRP* 3.8 36.1 - - + -
47B GLU 2.9 18.3 + - - +
48B VAL* 3.1 14.3 + - + +
50B ARG* 1.3 76.9 - - - +
52B PHE* 1.3 66.1 + - + +
54B LYS* 3.3 5.7 + - - +
55B VAL* 3.1 26.4 + - + +
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Residues in contact with PHE 52 (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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6B VAL* 6.5 0.7 - - + -
9B TRP* 4.3 18.2 - - + -
10B ILE* 6.0 2.0 - - + -
13B LEU* 4.0 26.7 - - + -
48B VAL* 3.1 22.9 + - + +
49B ARG* 3.8 7.0 - - - +
51B ILE* 1.3 80.9 - - + +
53B ALA* 1.3 66.9 + - - +
55B VAL* 3.3 7.0 + - - +
56B SER* 2.9 23.2 + - - -
63B VAL* 3.8 15.6 - - + +
66B ILE* 3.8 31.7 - - + +
67B TRP* 3.4 65.3 - + + +
70B VAL* 4.1 7.2 - - + -
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Residues in contact with ALA 53 (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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49B ARG 2.9 18.9 + - - +
50B ARG* 3.6 9.9 - - + +
52B PHE* 1.3 75.8 - - - +
54B LYS* 1.3 57.7 + - - +
56B SER* 3.1 10.1 + - - -
57B GLU* 2.9 28.6 + - - +
63B VAL* 4.4 6.6 - - - +
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Residues in contact with LYS 54 (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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25B SER* 3.8 15.0 - - - +
28B SER* 3.2 41.3 + - - +
29B VAL* 5.5 1.8 - - + +
50B ARG 3.1 13.3 + - - +
51B ILE* 3.7 4.5 - - - +
52B PHE 3.3 0.2 - - - -
53B ALA* 1.3 78.3 - - - +
55B VAL* 1.3 58.6 + - - +
57B GLU* 3.4 29.6 + - - +
58B LYS* 2.8 67.0 + - - +
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Residues in contact with VAL 55 (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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13B LEU* 4.2 24.0 - - + -
17B TYR* 3.5 37.0 - - + -
21B VAL* 4.1 17.5 - - + +
22B VAL* 5.0 4.9 - - + -
25B SER* 3.4 20.4 - - - +
51B ILE* 3.1 17.9 + - + +
52B PHE* 3.6 9.0 - - - +
54B LYS* 1.3 72.1 - - - +
56B SER* 1.3 59.5 + - - +
58B LYS 3.3 0.5 + - - -
59B THR* 2.5 39.2 + - + +
66B ILE* 4.0 7.0 - - + -
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Residues in contact with SER 56 (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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52B PHE 2.9 12.7 + - - -
53B ALA* 3.1 10.5 - - - -
55B VAL* 1.3 76.0 - - - +
57B GLU* 1.3 56.1 + - - +
59B THR* 2.9 5.1 + - - -
60B GLY* 2.6 35.9 + - - -
61B LYS 2.5 27.7 + - - -
62B ASN* 4.2 1.4 - - - -
63B VAL* 3.7 17.7 + - - +
66B ILE* 3.7 8.7 - - - +
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Residues in contact with GLU 57 (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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53B ALA 2.9 12.8 + - - +
54B LYS* 3.6 34.8 - - + +
56B SER* 1.3 76.8 + - - +
58B LYS* 1.3 63.5 + - + +
59B THR 3.2 3.5 + - - -
60B GLY* 3.8 6.4 + - - -
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Residues in contact with LYS 58 (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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21B VAL* 4.1 24.2 - - + +
24B GLU* 3.5 45.5 + - - +
25B SER* 3.7 15.9 - - - +
28B SER* 4.6 1.8 + - - -
54B LYS* 2.8 52.0 + - + +
55B VAL 3.3 3.3 + - - +
56B SER 3.2 0.4 - - - -
57B GLU* 1.3 76.5 + - + +
59B THR* 1.3 61.4 + - - +
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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