Contacts of the helix formed by residues 78 - 85 (chain H) in PDB entry 1U3H
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 78 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ASN* 4.5 6.7 - - + +
9G TYR* 3.9 9.9 - - + -
15H CYS* 4.7 1.6 - - - -
74H GLU* 2.7 38.7 + - + +
76H ASP 3.2 0.2 - - - -
77H THR* 1.3 84.1 - - - +
79H CYS* 1.3 59.5 + - - +
80H ARG 3.7 0.2 - - - -
82H ASN* 2.7 58.4 + - - +
0I GLY* 4.0 4.5 - - - +
1I ALA 3.8 24.0 - - - +
2I SER* 3.9 25.4 - - - +
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Residues in contact with CYS 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G TYR* 4.5 1.3 - - - -
15H CYS* 2.0 53.6 - - + -
17H PHE* 3.3 19.9 - - + -
24H ILE* 4.2 7.4 - - + -
26H TYR* 3.4 34.5 - - - -
74H GLU 3.0 3.4 + - - -
75H LEU* 3.2 14.4 - - - +
78H VAL* 1.3 76.6 - - - +
80H ARG* 1.3 67.5 + - - +
82H ASN* 3.9 0.5 - - - +
83H TYR* 3.0 19.1 + - - +
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Residues in contact with ARG 80 (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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17H PHE* 4.3 0.4 - - - -
21H THR* 2.6 44.0 + - + -
22H GLN* 4.1 5.9 + - - +
24H ILE* 3.7 20.4 - - + +
75H LEU* 3.1 15.6 + - - +
76H ASP* 2.6 46.6 + - - +
78H VAL 3.7 0.2 - - - -
79H CYS* 1.3 78.6 - - - +
81H TYR* 1.3 62.4 + - - +
83H TYR* 3.5 0.9 + - - +
84H GLU* 3.1 47.0 + - - +
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Residues in contact with TYR 81 (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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27E SER* 4.1 28.8 + - - -
28E ALA* 4.0 12.4 - - - +
68E LYS* 6.5 1.3 - - - -
99E ASN* 3.3 22.2 - - - -
76H ASP 3.1 13.1 + - - +
77H THR* 3.3 23.6 - - - +
79H CYS 3.1 0.4 - - - -
80H ARG* 1.3 75.9 - - - +
82H ASN* 1.3 68.2 + - - +
84H GLU* 2.8 77.9 + - - +
85H THR* 5.1 0.2 - - + -
-3I SER 4.9 0.9 + - - -
-2I ARG* 3.0 37.3 + - - +
-1I GLY* 4.3 0.7 - - - -
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Residues in contact with ASN 82 (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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9G TYR* 3.0 48.7 - - + +
24G PHE* 4.2 2.4 - - - -
52G ARG* 5.5 0.7 - - - -
78H VAL* 2.7 24.8 + - - +
81H TYR* 1.3 78.7 - - - +
83H TYR* 1.3 56.2 + - - +
85H THR* 2.5 42.4 + - - +
86H GLU* 3.0 6.4 + - - +
-1I GLY* 3.5 8.0 - - - -
0I GLY* 2.7 48.8 + - - -
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Residues in contact with TYR 83 (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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5G HIS* 3.8 23.4 + + + -
9G TYR* 4.3 0.4 + - - -
26G PHE* 4.7 6.1 - + - -
17H PHE* 3.4 54.7 - + + -
20H GLY* 3.7 24.7 + - - -
21H THR* 3.8 17.7 - - + -
79H CYS 3.0 17.8 + - - +
80H ARG 3.7 3.8 - - - +
82H ASN* 1.3 80.0 - - - +
84H GLU* 1.3 64.9 + - + +
86H GLU* 3.4 8.0 - - - +
87H VAL* 3.1 34.2 + - + +
91H LEU* 3.5 29.9 - - + +
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Residues in contact with GLU 84 (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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27E SER* 6.0 0.9 - - - -
51G LEU 5.4 0.9 - - - +
21H THR* 3.2 31.4 + - + -
80H ARG* 3.1 37.0 + - - +
81H TYR* 2.8 65.4 + - - +
83H TYR* 1.3 79.1 - - + +
85H THR* 1.3 62.6 + - - +
87H VAL* 3.7 23.6 - - + +
88H PRO* 3.9 15.0 - - - +
-3I SER 3.7 20.9 + - - +
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Residues in contact with THR 85 (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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52G ARG* 3.1 54.3 + - + +
53G SER 5.3 0.4 - - - +
81H TYR* 5.1 0.2 - - + -
82H ASN* 2.5 36.5 + - - +
84H GLU* 1.3 83.8 - - - +
86H GLU* 1.3 53.3 + - - +
87H VAL 3.6 0.4 - - - -
88H PRO* 3.6 11.6 - - - +
89H THR* 2.8 25.0 + - - +
-3I SER 4.2 11.4 - - - +
-2I ARG 4.5 1.1 - - - +
-1I GLY* 4.1 26.7 - - - +
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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