Contacts of the helix formed by residues 85 - 100 (chain F) 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 ASP 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F VAL* 4.4 0.9 - - - -
83F CYS* 3.4 12.6 - - - -
84F ARG* 1.3 79.4 - - - +
86F PRO* 1.3 69.5 - - - +
87F MET* 3.0 24.4 + - - +
88F GLN* 3.0 42.1 + - - +
89F VAL 3.6 0.9 + - - -
91F ARG* 4.0 17.3 + - - -
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Residues in contact with PRO 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA 5.5 0.2 - - - +
30F VAL* 3.7 22.5 - - + +
31F ASP* 3.5 26.2 - - - +
34F VAL* 4.0 19.9 - - + -
84F ARG 3.8 8.3 - - - +
85F ASP* 1.3 89.6 - - - +
87F MET* 1.3 65.2 + - + +
89F VAL* 3.1 15.2 + - + +
90F LEU* 3.1 20.2 + - + +
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Residues in contact with MET 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ASP* 3.0 15.7 + - - +
86F PRO* 1.3 80.4 - - + +
88F GLN* 1.3 56.5 + - - +
90F LEU* 3.3 27.4 + - + +
91F ARG* 2.8 56.3 + - + +
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Residues in contact with GLN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F MET* 3.8 21.5 - - + +
83F CYS* 4.2 14.8 - - - +
84F ARG 5.4 0.6 - - - +
85F ASP* 3.0 33.0 + - + +
87F MET* 1.3 76.2 - - - +
89F VAL* 1.3 64.9 + - - +
91F ARG* 3.4 26.9 + - - +
92F GLU* 3.1 27.9 + - + +
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Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL* 3.7 29.4 - - + -
33F ILE* 5.5 0.7 - - + -
34F VAL* 5.0 2.0 - - + -
40F PRO* 3.7 33.0 - - + -
42F LEU* 6.0 1.6 - - + -
80F MET* 4.0 11.0 - - - -
83F CYS* 3.9 15.9 - - - -
85F ASP 4.0 1.8 - - - +
86F PRO* 3.1 11.1 + - + +
88F GLN* 1.3 76.1 - - - +
90F LEU* 1.3 62.7 + - - +
92F GLU* 3.1 5.0 + - - +
93F ILE* 3.0 25.8 + - + +
107F LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ASP 5.7 0.7 - - - +
26F ILE* 4.3 12.6 - - + -
27F ALA* 4.5 22.2 - - + +
30F VAL* 4.1 23.3 - - + -
86F PRO* 3.1 18.8 + - + +
87F MET* 3.3 37.0 + - + +
89F VAL* 1.3 74.6 - - - +
91F ARG* 1.3 63.1 + - + +
93F ILE* 3.3 16.7 + - + +
94F VAL* 3.2 26.0 + - - +
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ASP* 4.0 9.1 + - - -
87F MET* 2.8 47.6 + - + +
88F GLN* 3.6 35.1 - - - +
90F LEU* 1.3 78.1 - - + +
92F GLU* 1.3 58.3 + - - +
94F VAL* 3.2 10.4 + - - +
95F ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.5 15.6 - - + +
76F TRP* 2.8 31.7 + - + +
77F LYS* 3.0 29.8 + - - +
80F MET* 3.8 26.6 - - + +
88F GLN* 3.1 18.7 + - + +
89F VAL 3.1 8.0 + - - +
91F ARG* 1.3 74.8 - - - +
93F ILE* 1.3 60.3 + - - +
95F ALA* 3.7 6.3 - - - +
96F CYS* 2.8 32.9 + - - +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ILE* 4.6 11.2 - - + -
42F LEU* 3.5 27.1 - - + +
89F VAL* 3.0 28.5 + - + +
90F LEU* 3.3 28.0 + - + +
92F GLU* 1.3 75.3 - - - +
94F VAL* 1.3 63.1 + - + +
96F CYS* 3.9 1.0 - - - +
97F THR* 2.8 38.4 + - + +
105F VAL* 5.8 0.4 - - + -
107F LEU* 4.5 15.7 - - + -
123F VAL* 4.3 26.7 - - + +
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LEU* 3.2 16.5 + - + +
91F ARG* 3.5 9.6 - - - +
92F GLU 3.2 0.2 - - - -
93F ILE* 1.3 78.4 - - + +
95F ALA* 1.3 57.8 + - - +
97F THR* 3.1 7.1 + - - -
98F LYS* 3.0 38.7 + - + +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TRP* 3.7 16.4 - - + -
77F LYS* 4.8 4.0 - - - +
91F ARG 2.9 16.7 + - - +
92F GLU* 3.2 14.1 + - - +
94F VAL* 1.3 77.8 - - - +
96F CYS* 1.3 63.4 + - - +
98F LYS* 3.4 8.6 + - - +
99F ALA* 3.0 24.1 + - - +
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Residues in contact with CYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 4.1 8.1 - - + -
44F PHE* 4.2 13.5 - - - -
76F TRP* 3.6 47.7 - - + -
92F GLU 2.8 21.2 + - - +
93F ILE* 3.9 3.4 - - - +
95F ALA* 1.3 71.9 - - - +
97F THR* 1.3 56.7 + - - +
99F ALA* 3.2 4.3 + - - +
100F PHE* 2.9 29.3 + - - +
105F VAL* 3.8 31.2 - - + -
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE* 2.8 34.1 + - + +
94F VAL* 3.1 11.4 + - - -
96F CYS* 1.3 71.5 - - - +
98F LYS* 1.3 64.4 + - - +
100F PHE 4.2 4.9 - - - -
101F PRO* 3.1 27.5 - - - +
105F VAL* 4.1 14.1 - - + -
123F VAL* 5.1 2.0 - - + +
124F GLN* 3.2 41.6 - - + +
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Residues in contact with LYS 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F VAL* 3.0 26.0 + - + +
95F ALA* 3.6 7.9 - - - +
96F CYS 3.2 0.2 - - - -
97F THR* 1.3 78.5 + - - +
99F ALA* 1.3 62.6 + - - +
101F PRO* 3.5 12.9 - - - +
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.8 28.1 - - + +
76F TRP* 3.7 25.8 - - + -
95F ALA 3.0 16.1 + - - +
96F CYS 3.2 2.2 + - - +
98F LYS* 1.3 76.9 - - - +
100F PHE* 1.3 68.0 + - + +
101F PRO* 3.4 6.4 - - - +
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Residues in contact with PHE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.5 2.0 - - + -
5C THR* 3.5 28.5 - - - -
6C PRO* 4.0 5.8 - - + -
7C VAL* 4.3 13.0 - - + -
140C VAL* 3.7 31.0 - - + -
44F PHE* 3.5 45.3 - + + -
76F TRP* 3.9 13.7 - + - -
96F CYS* 2.9 13.5 + - - +
97F THR* 3.3 6.2 - - - +
99F ALA* 1.3 86.6 - - + +
101F PRO* 1.3 62.2 - - - +
102F ASP 3.2 4.8 + - - -
103F ALA* 3.2 21.7 + - + +
105F VAL* 4.6 2.2 - - + +
124F GLN* 2.9 19.2 + - - -
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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