Contacts of the helix formed by residues 49 - 62 (chain U) in PDB entry 5OOM
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 49 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389 ALA* 3.7 28.5 - - + -
399 LYS 4.3 14.1 - - - +
419 ILE* 3.9 15.0 - - + +
2418A A 4.0 5.4 - - - +
2419A C 3.4 21.5 - - - -
44U ILE* 4.0 3.0 - - - +
47U GLU 3.4 3.2 + - - +
48U MET* 1.3 78.7 - - - +
50U ARG* 1.3 64.9 + - - +
51U VAL 3.3 3.1 + - - -
52U ASP* 3.2 32.4 + - - +
53U LEU* 3.2 21.7 + - - +
70U THR* 5.5 0.9 - - - -
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Residues in contact with ARG 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2373A A 2.9 42.8 + - - -
2374A A 5.8 0.2 + - - -
2418A A 3.7 37.6 + - - +
2419A C 2.8 32.9 + - - +
2420A U 5.8 0.4 + - - -
49U THR* 1.3 72.6 - - - +
51U VAL* 1.3 60.3 + - + +
53U LEU* 3.4 3.4 + - - +
54U ARG* 3.0 29.0 + - - +
68U VAL* 3.3 49.1 + - + +
69U ARG* 5.0 0.4 - - - +
70U THR* 3.2 33.4 + - + +
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Residues in contact with VAL 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419 ILE* 3.9 17.3 - - + -
529 GLN* 4.0 23.1 - - - +
579 VAL* 3.7 23.3 - - + -
2418A A 3.9 31.2 - - - -
49U THR* 3.3 3.5 + - - +
50U ARG* 1.3 74.2 - - + +
52U ASP* 1.3 66.7 + - - +
54U ARG* 3.2 11.5 + - + +
55U ASN* 2.9 36.3 + - - +
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Residues in contact with ASP 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419 ILE* 5.2 2.1 - - - +
579 VAL* 4.3 4.3 - - - +
589 PRO* 3.4 35.2 - - - +
609 PHE* 3.4 12.0 - - + -
7U TYR* 4.6 5.5 + - - -
24U PHE* 4.2 18.2 - - + -
47U GLU 4.4 3.1 - - - +
48U MET* 4.0 11.4 - - + +
49U THR* 3.2 36.9 + - - +
51U VAL* 1.3 78.5 - - - +
53U LEU* 1.3 58.4 + - - +
55U ASN* 4.5 1.3 - - - -
56U TYR* 2.9 30.4 + - - +
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Residues in contact with LEU 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U ILE* 3.6 31.6 - - + -
42U PHE* 5.0 0.7 - - + -
44U ILE* 3.6 23.1 - - + -
48U MET* 3.7 15.5 - - + +
49U THR 3.2 15.6 + - - +
50U ARG* 3.7 5.8 - - - +
51U VAL 3.1 0.4 - - - -
52U ASP* 1.3 78.2 - - - +
54U ARG* 1.3 64.6 + - - +
56U TYR* 4.6 0.7 - - + -
57U LEU* 3.0 34.2 + - + +
65U VAL* 5.4 0.4 - - + -
68U VAL* 3.8 17.3 - - + -
95U ALA* 4.3 4.0 - - + -
97U VAL* 3.6 31.0 - - + -
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Residues in contact with ARG 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50U ARG* 3.0 16.5 + - - +
51U VAL* 3.2 15.0 + - - +
53U LEU* 1.3 79.4 - - - +
55U ASN* 1.3 66.3 + - - +
57U LEU* 3.9 1.4 - - - +
58U GLU* 3.0 40.6 + - + +
65U VAL* 3.0 48.6 + - + +
66U ALA* 3.0 28.2 + - - +
67U ALA* 4.0 7.7 - - - +
68U VAL* 4.4 9.3 - - + +
314s GLN* 4.2 33.6 - - - +
315s ASN* 4.4 4.5 + - - +
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Residues in contact with ASN 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579 VAL* 3.7 23.0 - - - +
589 PRO 4.2 5.5 - - - +
599 GLU* 5.8 1.3 - - - -
609 PHE* 3.8 26.0 - - + +
51U VAL* 2.9 23.2 + - - +
52U ASP* 4.5 0.5 + - - -
54U ARG* 1.3 87.4 - - - +
56U TYR* 1.3 57.7 + - - +
58U GLU* 3.8 8.3 - - - +
59U GLY* 2.9 25.6 + - - -
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Residues in contact with TYR 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609 PHE* 3.7 26.0 - + + -
22U THR* 3.6 15.3 - - + -
24U PHE* 3.2 27.6 + + - -
26U ILE* 3.6 34.0 - - + +
48U MET* 3.5 22.2 - - + -
52U ASP 2.9 20.7 + - - +
53U LEU 3.6 4.5 - - - +
54U ARG 3.2 0.4 - - - -
55U ASN* 1.3 76.7 - - - +
57U LEU* 1.3 62.8 + - + +
60U ILE* 3.1 52.4 + - + +
61U TYR* 4.4 7.2 - + - -
106Y LEU* 3.3 22.1 - - + +
110Y ASN* 3.4 12.5 + - - -
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Residues in contact with LEU 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U ILE* 4.6 4.0 - - + -
42U PHE* 3.9 34.8 - - + -
53U LEU* 3.0 42.1 + - + +
56U TYR* 1.3 77.1 - - + +
58U GLU* 1.3 64.0 + - - +
61U TYR* 3.3 20.3 + - + +
62U ASN 3.1 18.9 + - - -
63U VAL* 3.2 19.5 + - + -
65U VAL* 3.8 28.9 - - + -
97U VAL* 4.4 2.5 - - + -
64Y LEU* 4.8 0.2 - - + -
67Y PHE* 4.0 22.2 - - + -
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Residues in contact with GLU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U ARG* 3.0 33.1 + - + +
55U ASN* 4.0 8.5 - - - +
57U LEU* 1.3 79.2 - - - +
59U GLY* 1.3 62.8 + - - +
62U ASN* 3.4 21.8 + - - +
63U VAL 2.9 23.4 + - - +
64U PRO* 3.3 4.7 - - - +
65U VAL* 2.9 18.6 + - + +
315s ASN* 2.9 23.1 + - - +
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Residues in contact with GLY 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609 PHE* 5.3 4.0 - - - -
629 VAL* 3.9 23.4 - - - +
55U ASN 2.9 17.6 + - - -
58U GLU* 1.3 80.7 - - - +
60U ILE* 1.3 64.4 + - - +
62U ASN* 4.3 8.1 + - - +
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Residues in contact with ILE 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609 PHE* 4.9 3.8 - - + -
629 VAL* 3.8 24.9 - - + +
22U THR* 4.4 3.6 - - - +
56U TYR* 3.1 49.3 + - + +
59U GLY* 1.3 79.9 - - - +
61U TYR* 1.3 74.0 + - + +
62U ASN* 3.6 4.2 + - - -
66Y GLU* 4.2 2.6 - - - +
103Y TYR* 3.7 26.9 - - + -
106Y LEU* 3.9 9.0 - - + -
107Y LYS* 3.8 39.6 + - + +
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Residues in contact with TYR 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U TYR* 4.4 10.3 - + - -
57U LEU* 3.3 21.8 + - + +
60U ILE* 1.3 91.6 - - + +
62U ASN* 1.3 63.5 + - - +
63U VAL* 3.4 14.9 + - + -
63Y GLY* 2.7 37.0 + - - +
66Y GLU* 3.3 51.8 + - + +
67Y PHE* 3.6 30.4 - + + -
107Y LYS* 3.4 25.1 + - + -
110Y ASN* 2.9 39.9 + - - +
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Residues in contact with ASN 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57U LEU 3.1 3.6 + - - -
58U GLU* 3.4 20.9 + - - +
59U GLY 4.3 6.8 + - - +
60U ILE 3.6 4.6 + - - -
61U TYR* 1.3 80.1 - - - +
63U VAL* 1.3 59.2 - - - +
64U PRO* 3.6 8.5 - - - +
63Y GLY* 4.4 9.0 + - - +
66Y GLU* 6.0 0.4 + - - -
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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