Contacts of the helix formed by residues 49 - 63 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47K ASP 3.2 4.4 + - - -
48K TYR* 1.3 75.5 - - + +
50K GLN* 1.3 64.5 + - - +
51K GLN* 2.7 26.5 + - - +
52K VAL* 3.2 29.7 + - + +
53K PHE* 3.1 18.9 + - - +
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Residues in contact with GLN 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LYS* 3.5 28.8 + - - +
48K TYR 3.2 5.3 + - - +
49K ASP* 1.3 73.4 + - - +
51K GLN* 1.3 62.6 + - - +
53K PHE* 3.0 17.5 + - - +
54K GLU* 2.9 54.3 + - - +
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Residues in contact with GLN 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ASP* 2.7 16.0 + - - +
50K GLN* 1.3 74.1 - - - +
52K VAL* 1.3 56.5 + - + +
54K GLU* 3.2 14.9 + - - +
55K ARG* 2.8 48.7 + - - +
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Residues in contact with VAL 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J GLU* 3.6 28.5 - - + +
32J SER* 5.3 3.8 - - - -
48K TYR* 3.8 27.0 - - + +
49K ASP* 3.2 34.7 + - + +
51K GLN* 1.3 76.8 - - + +
53K PHE* 1.3 63.0 + - - +
55K ARG* 3.3 27.9 + - - +
56K HIS* 3.1 19.1 + - - +
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Residues in contact with PHE 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LYS* 3.9 34.3 - - + -
36K VAL 3.4 27.8 - - - -
37K CYS* 4.1 2.7 - - - -
38K PRO* 4.3 4.3 - - + -
44K PHE* 3.6 42.0 - + - -
48K TYR* 4.1 13.6 - - + -
49K ASP 3.1 10.9 + - - +
50K GLN* 3.0 23.8 + - - +
52K VAL* 1.3 75.3 - - - +
54K GLU* 1.3 68.3 + - + +
56K HIS* 2.7 24.0 + - - +
57K VAL* 3.1 31.9 + - + +
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Residues in contact with GLU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K GLN* 2.9 44.8 + - - +
51K GLN* 3.7 16.5 - - - +
53K PHE* 1.3 83.1 - - + +
55K ARG* 1.3 57.7 + - - +
57K VAL* 3.2 6.8 + - - +
58K GLN* 2.8 32.1 + - - +
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Residues in contact with ARG 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J LYS 5.7 0.2 - - - -
28J GLU* 3.3 59.3 + - - +
29J HIS* 4.9 3.1 - - - +
31J GLU* 4.7 2.2 + - - -
32J SER* 4.0 14.8 - - - +
51K GLN* 2.8 29.4 + - - +
52K VAL* 3.5 43.8 - - + +
54K GLU* 1.3 77.3 - - - +
56K HIS* 1.3 60.3 + - - +
58K GLN* 3.4 7.1 + - + +
59K THR* 3.1 28.9 + - - +
103K CL 3.3 29.6 - - - +
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Residues in contact with HIS 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J SER* 3.5 31.1 + - - +
33J HIS* 4.9 4.4 + - - -
34J TRP 4.7 8.2 + - - -
37K CYS* 2.9 18.2 - - + +
40K CYS* 3.6 7.6 - - - -
42K GLU* 4.0 15.9 - - + +
44K PHE* 3.9 21.7 - + + -
52K VAL 3.1 10.6 + - - +
53K PHE* 2.7 16.4 + - - +
55K ARG* 1.3 70.8 - - - +
57K VAL* 1.3 71.5 + - + +
59K THR* 3.4 9.0 + - - -
60K HIS* 3.1 19.0 + + - -
102K ZN 1.8 38.2 - - - -
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Residues in contact with VAL 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K CYS* 3.9 16.4 - - - -
38K PRO* 4.0 14.8 - - + -
39K MET* 4.2 20.2 - - + -
53K PHE* 3.1 39.6 + - + +
54K GLU* 3.8 7.0 - - + +
56K HIS* 1.3 80.8 - - + +
58K GLN* 1.3 64.9 + - - +
60K HIS* 3.1 24.2 + - - +
61K PHE* 3.8 16.4 + - + -
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Residues in contact with GLN 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K GLU 2.8 17.8 + - - +
55K ARG* 3.8 9.4 - - + +
57K VAL* 1.3 79.0 - - - +
59K THR* 1.3 56.2 + - - +
61K PHE* 2.9 41.1 + - - +
62K ASP* 3.1 39.6 + - - +
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Residues in contact with THR 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J HIS* 4.1 15.0 + - + -
32J SER* 2.6 30.5 + - - +
33J HIS* 3.6 23.1 - - + +
55K ARG* 3.1 14.1 + - - +
56K HIS 3.7 6.5 - - - -
57K VAL 3.2 0.2 - - - -
58K GLN* 1.3 71.7 - - - +
60K HIS* 1.3 68.3 + - + +
61K PHE 2.9 2.8 + - - -
62K ASP* 3.8 10.9 + - + +
63K GLN* 2.9 49.6 + - + +
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Residues in contact with HIS 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K CYS* 3.6 8.3 - - - -
39K MET* 3.9 28.7 - - + +
40K CYS* 3.2 20.6 - - + -
56K HIS* 2.7 31.5 + + - -
57K VAL* 3.1 13.4 + - - +
59K THR* 1.3 77.7 - - + +
61K PHE* 1.3 60.4 + - - +
63K GLN* 4.3 20.8 + - - +
65K VAL* 5.3 3.3 - - - +
102K ZN 1.9 37.4 - - - -
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Residues in contact with PHE 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K MET* 3.5 33.4 - - + -
57K VAL* 4.0 24.5 - - + -
58K GLN* 2.9 31.6 + - - +
59K THR 2.9 0.4 - - - -
60K HIS* 1.3 77.2 - - - +
62K ASP* 1.3 66.9 + - - +
63K GLN 3.0 4.9 + - - +
64K ASN* 3.2 21.3 + - - -
65K VAL* 5.4 0.3 - - - +
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Residues in contact with ASP 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 3.8 29.5 - - + +
29J HIS* 5.5 3.2 + - + -
58K GLN* 3.1 40.7 + - - +
59K THR* 3.8 13.3 + - - +
61K PHE* 1.3 68.6 - - - +
63K GLN* 1.3 52.1 + - - +
64K ASN* 2.3 31.9 + - - +
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Residues in contact with GLN 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J CYS* 3.5 28.9 - - + +
14J GLU 5.1 0.6 + - - +
15J LEU* 4.1 15.0 - - + -
33J HIS* 3.6 11.7 + - - -
59K THR* 2.9 38.1 + - + +
60K HIS* 4.3 14.8 + - - +
61K PHE 3.0 4.2 + - - +
62K ASP* 1.3 70.7 - - - +
64K ASN* 1.3 53.9 + - - +
65K VAL* 2.7 33.8 - - + +
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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