Contacts of the helix formed by residues 69 - 75 (chain H) in PDB entry 1UW9
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 VAL 69 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H PHE* 3.8 3.4 - - - -
63H THR 6.0 0.4 - - - +
65H THR* 4.1 11.4 - - + +
67H THR 3.8 9.4 - - - +
68H THR* 1.3 83.5 - - - +
70H TRP* 1.3 63.0 + - - +
71H THR* 3.5 18.6 - - - +
72H ASP* 3.4 35.5 + - - +
1478H EDO 3.2 7.6 + - - +
175R LYS* 3.9 23.3 - - + -
176R PRO* 4.2 2.2 - - + -
404R GLY* 4.2 6.1 - - - -
407R LEU* 3.4 30.5 - - + +
408R GLY 4.1 1.8 - - - +
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Residues in contact with TRP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H PHE* 3.5 41.6 - + + +
69H VAL* 1.3 69.5 - - - +
71H THR* 1.3 87.0 + - + +
72H ASP 3.1 2.9 - - - -
73H GLY* 3.1 12.7 + - - -
74H LEU* 3.7 26.5 - - + -
75P MET* 3.8 22.9 - - + -
78P LEU* 3.6 31.9 - - + +
79P PRO* 3.8 15.7 - - + -
81P PHE* 3.5 30.4 - + + -
187R ARG* 5.2 5.4 - - + -
188R ALA* 5.2 3.4 - - + -
191R GLU* 5.8 2.7 - - + -
407R LEU 3.1 28.2 + - - -
409R HIS 4.7 0.2 - - - -
412R GLY* 4.0 7.3 - - - -
413R ASN* 2.8 38.4 + - - -
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H VAL* 3.5 9.9 - - - +
70H TRP* 1.3 110.4 - - + +
72H ASP* 1.3 64.1 + - - +
73H GLY 3.0 2.7 - - - -
74H LEU* 3.1 24.6 + - + +
75H THR* 3.9 1.0 + - - +
175R LYS 2.5 32.1 + - - +
176R PRO* 3.3 5.7 - - - +
180R LEU* 3.9 15.8 - - + +
188R ALA* 4.6 9.4 - - + -
407R LEU* 3.8 14.2 - - + +
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Residues in contact with ASP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H THR* 5.0 1.7 - - - +
69H VAL* 3.4 25.1 + - - +
70H TRP 3.1 0.6 - - - +
71H THR* 1.3 76.9 + - - +
73H GLY* 1.3 57.1 + - - +
75H THR* 3.0 34.3 + - - +
77H LEU* 3.6 26.3 + - + +
1478H EDO 2.6 38.3 + - - -
176R PRO* 3.5 22.6 - - - +
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Residues in contact with GLY 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H TRP 3.1 6.3 + - - -
71H THR 3.0 2.0 - - - -
72H ASP* 1.3 78.1 - - - +
74H LEU* 1.3 59.4 + - - +
75H THR 3.2 2.6 - - - +
39P ILE* 3.4 13.5 - - - +
81P PHE* 3.4 26.2 - - - -
112P ASN* 3.4 18.6 + - - +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H TRP* 3.7 29.4 - - + -
71H THR* 3.1 18.4 + - + +
73H GLY* 1.3 76.9 - - - +
75H THR* 1.3 59.0 + - - +
39P ILE* 5.0 0.9 - - - -
79P PRO* 4.2 6.7 - - + -
81P PHE* 3.8 17.0 - - + -
110P PHE* 4.0 36.8 - - + +
111P ASP 4.5 0.5 - - - +
112P ASN* 3.5 15.7 - - - -
115P GLN* 3.4 20.2 - - - +
180R LEU* 4.5 5.4 - - + -
184R ASN* 3.8 39.6 + - + +
187R ARG* 4.7 8.1 - - - -
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H THR 4.3 2.5 - - - +
72H ASP* 3.0 21.1 + - - +
73H GLY* 3.9 1.6 - - - +
74H LEU* 1.3 80.2 - - - +
76H SER* 1.3 72.3 + - - +
77H LEU* 4.0 5.7 + - + +
80H TYR* 3.3 15.2 - - + -
112P ASN* 3.1 26.8 + - - +
115P GLN* 3.5 14.1 + - - +
176R PRO* 4.2 24.0 - - + -
179R GLY* 2.9 30.8 + - - +
180R LEU* 4.5 1.6 - - + -
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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