Contacts of the helix formed by residues 49 - 64 (chain B) in PDB entry 4BMJ
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASP 3.4 5.0 + - - -
48B TYR* 1.3 74.3 - - + +
50B GLN* 1.3 55.9 + - - +
51B GLN* 3.4 11.9 + - - +
52B VAL* 2.8 48.5 + - + +
53B PHE* 2.7 34.7 + - - +
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Residues in contact with GLN 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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35B LYS* 2.6 31.8 + - - +
48B TYR 3.3 4.7 + - - +
49B ASP* 1.3 70.0 + - - +
51B GLN* 1.3 69.0 + - - +
53B PHE* 3.0 13.1 + - - +
54B GLU* 2.7 63.4 + - - +
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Residues in contact with GLN 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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49B ASP* 3.4 12.1 + - - +
50B GLN* 1.3 77.5 - - - +
52B VAL* 1.3 64.5 + - + +
54B GLU* 3.2 10.4 + - - +
55B ARG* 2.8 49.1 + - - +
103B CL 4.3 9.5 - - - +
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Residues in contact with VAL 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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28A GLU* 5.6 0.4 - - - +
31A GLU* 3.8 24.7 - - + +
32A SER* 5.6 2.1 - - - -
48B TYR* 3.6 27.5 - - + +
49B ASP* 2.8 43.9 + - + +
51B GLN* 1.3 73.0 - - + +
53B PHE* 1.3 66.1 + - - +
55B ARG* 3.2 27.1 + - - +
56B HIS* 3.2 17.2 + - - +
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Residues in contact with PHE 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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35B LYS* 3.6 36.3 - - + -
36B VAL 3.7 19.5 - - - -
37B CYS* 4.1 7.9 - - - -
38B PRO* 4.6 2.5 - - + -
44B PHE* 3.5 43.7 - + - -
48B TYR* 4.0 12.5 - - + -
49B ASP 2.7 16.5 + - - +
50B GLN* 3.4 20.2 - - - +
52B VAL* 1.3 73.0 - - - +
54B GLU* 1.3 62.7 + - + +
56B HIS* 2.9 24.8 + - - +
57B VAL* 3.2 31.3 + - + +
42C GLU* 4.1 10.8 - - - -
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Residues in contact with GLU 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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50B GLN* 2.7 55.3 + - - +
51B GLN* 3.7 8.3 - - - +
53B PHE* 1.3 76.8 - - + +
55B ARG* 1.3 57.2 + - - +
57B VAL* 3.4 7.3 + - - +
58B GLN* 2.8 31.0 + - - +
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Residues in contact with ARG 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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25A LYS 5.5 0.7 - - - -
28A GLU* 3.3 61.2 + - - +
29A HIS* 4.7 3.8 - - - +
31A GLU* 4.8 3.4 + - - -
32A SER* 4.1 13.0 - - - -
51B GLN* 2.8 33.0 + - - +
52B VAL* 3.5 36.7 - - + +
53B PHE 3.1 0.6 + - - -
54B GLU* 1.3 72.2 - - - +
56B HIS* 1.3 64.2 + - - +
58B GLN* 3.1 7.9 + - + +
59B THR* 2.9 27.9 + - - +
103B CL 3.2 29.8 - - - +
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Residues in contact with HIS 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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32A SER* 3.2 36.0 + - - +
33A HIS* 5.4 3.4 - - - -
34A TRP 4.7 7.0 + - - -
37B CYS* 3.2 15.6 - - + +
40B CYS* 3.8 6.5 - - - -
42B GLU* 4.0 15.9 - - + -
44B PHE* 3.9 22.2 - + + -
48B TYR* 6.1 0.4 - - + -
52B VAL 3.2 7.7 + - - +
53B PHE* 2.9 10.6 + - - +
55B ARG* 1.3 74.2 - - - +
57B VAL* 1.3 89.6 + - + +
59B THR* 3.0 18.2 + - - -
60B HIS* 3.6 12.2 + + - -
102B ZN 1.9 36.6 - - - -
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Residues in contact with VAL 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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37B CYS* 4.0 7.6 - - - -
38B PRO* 3.5 28.9 - - + -
39B MET* 4.2 9.9 - - + -
53B PHE* 3.2 26.9 + - + +
54B GLU* 3.9 7.9 - - - +
56B HIS* 1.3 91.0 - - + +
58B GLN* 1.3 67.2 + - - +
60B HIS* 3.1 21.9 + - - +
61B PHE* 4.1 7.8 + - + -
34C TRP* 4.0 26.9 - - + -
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Residues in contact with GLN 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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54B GLU 2.8 18.4 + - - +
55B ARG* 3.4 8.7 - - + +
56B HIS 3.1 0.2 - - - -
57B VAL* 1.3 79.9 - - - +
59B THR* 1.3 62.2 + - - +
61B PHE* 3.0 24.9 + - - +
62B ASP* 3.2 30.9 + - - +
27C GLU* 3.0 37.1 + - - +
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Residues in contact with THR 59 (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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29A HIS* 4.1 13.5 + - + -
32A SER* 2.5 29.6 + - - +
33A HIS* 3.3 37.0 - - + +
55B ARG* 2.9 14.7 + - - +
56B HIS 3.0 8.7 + - - -
58B GLN* 1.3 76.3 - - - +
60B HIS* 1.3 64.6 + - - +
62B ASP* 3.8 11.8 + - + -
63B GLN* 2.9 32.3 + - + +
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Residues in contact with HIS 60 (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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37B CYS* 3.7 4.3 - - - -
39B MET* 3.4 36.9 - - + +
40B CYS* 3.2 20.1 - - + +
56B HIS* 3.2 15.8 + + - -
57B VAL 3.1 17.7 + - - +
59B THR* 1.3 78.2 - - - +
61B PHE* 1.3 61.0 + - + +
63B GLN* 3.7 10.0 + - - +
64B ASN* 2.8 27.7 - - - +
102B ZN 2.0 37.4 - - - -
104B CL 3.6 21.9 - - + +
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Residues in contact with PHE 61 (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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39B MET* 4.0 18.2 - - + -
57B VAL* 4.1 13.5 - - + -
58B GLN* 3.0 27.5 + - - +
60B HIS* 1.3 74.1 - - - +
62B ASP* 1.3 68.9 + - - +
63B GLN 3.0 1.6 - - - -
64B ASN* 2.7 18.2 + - - -
65B VAL* 3.5 9.9 + - - +
11C PRO* 6.4 0.2 - - + -
23C GLN* 4.0 5.5 + - - +
26C PHE* 4.5 11.9 - + - -
27C GLU* 3.3 50.9 - - + +
30C VAL* 3.9 38.8 - - + -
31C GLU* 5.8 0.2 - - + -
34C TRP* 4.2 22.2 - + - -
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Residues in contact with ASP 62 (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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15A LEU* 3.6 25.7 - - + +
29A HIS* 5.9 1.1 - - + +
58B GLN* 3.2 41.0 + - - +
59B THR* 3.8 11.6 + - + +
61B PHE* 1.3 77.1 - - - +
63B GLN* 1.3 62.4 + - - +
65B VAL* 3.3 26.6 - - - +
27C GLU* 4.5 4.2 + - - +
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Residues in contact with GLN 63 (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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12A LEU 5.5 0.2 - - - +
13A CYS* 3.7 25.7 - - + +
14A GLU* 5.2 8.7 + - - +
15A LEU* 4.3 15.5 - - + +
33A HIS* 2.9 32.6 + - + -
59B THR* 2.9 27.4 + - + +
60B HIS* 3.7 21.1 + - - +
61B PHE 2.9 0.6 + - - -
62B ASP* 1.3 75.6 - - - +
64B ASN* 1.3 73.7 + - - +
65B VAL 3.6 5.4 + - - +
67B ASN* 5.7 0.2 + - - -
104B CL 3.9 14.3 - - - +
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Residues in contact with ASN 64 (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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60B HIS 2.8 20.3 - - - +
61B PHE* 2.7 16.5 + - - +
63B GLN* 1.3 88.8 + - - +
65B VAL* 1.3 61.1 + - - +
66B LEU 3.4 2.6 + - - -
104B CL 4.2 9.4 - - - +
8C LYS* 3.9 10.0 + - - -
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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