Contacts of the helix formed by residues 85 - 100 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C VAL* 4.4 1.7 - - - +
83C CYS* 3.3 11.2 - - - -
84C ARG* 1.3 77.0 - - - +
86C PRO* 1.3 69.4 - - - +
87C MET* 3.0 23.3 + - - +
88C GLN* 3.1 41.8 + - - +
89C VAL* 3.5 2.1 + - - +
91C ARG* 4.0 16.3 + - - -
7O THR* 3.8 31.1 + - - +
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA 5.5 0.7 - - - +
30C VAL* 3.7 21.6 - - + +
31C ASP* 3.5 25.4 - - - +
34C VAL* 4.1 18.3 - - + -
84C ARG 3.7 8.7 - - - +
85C ASP* 1.3 89.3 - - - +
87C MET* 1.3 66.8 + - + +
89C VAL* 3.1 7.1 + - + +
90C LEU* 3.0 30.1 + - + +
7O THR* 4.7 7.0 - - + -
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Residues in contact with MET 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 3.0 15.7 + - - +
86C PRO* 1.3 80.7 - - + +
88C GLN* 1.3 57.7 + - - +
90C LEU* 3.3 26.7 + - + +
91C ARG* 2.9 56.1 + - + +
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C MET* 3.7 23.9 - - + +
83C CYS* 4.0 18.7 - - - +
84C ARG 5.5 0.6 - - - +
85C ASP* 3.1 33.5 + - + +
87C MET* 1.3 79.1 - - - +
89C VAL* 1.3 60.5 + - - +
91C ARG* 3.4 26.9 + - + +
92C GLU* 3.1 20.6 + - + +
7O THR 5.7 0.6 + - - -
9O ALA* 5.7 6.9 - - - +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.7 29.2 - - + -
33C ILE* 5.4 0.7 - - + -
34C VAL* 5.0 3.6 - - + -
40C PRO* 3.8 32.5 - - + -
42C LEU* 4.8 1.3 - - + +
80C MET* 4.0 11.2 - - - -
83C CYS* 4.0 8.1 - - - -
85C ASP 3.9 12.8 - - - +
86C PRO* 3.1 7.3 + - + +
88C GLN* 1.3 75.2 - - - +
90C LEU* 1.3 58.6 + - - +
92C GLU* 3.1 4.7 + - - +
93C ILE* 3.0 30.2 + - + +
107C LEU* 3.8 29.2 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASP 5.7 0.9 - - - +
26C ILE* 4.3 12.1 - - + -
27C ALA* 4.5 21.8 - - + -
30C VAL* 4.1 22.9 - - + -
86C PRO* 3.0 22.7 + - + +
87C MET* 3.7 35.4 - - + +
88C GLN 3.3 0.2 - - - -
89C VAL* 1.3 74.1 - - - +
91C ARG* 1.3 62.4 + - + +
93C ILE* 3.3 18.5 + - + +
94C VAL* 3.2 26.9 + - - +
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 4.0 9.5 + - - -
87C MET* 2.9 49.7 + - + +
88C GLN* 3.6 34.4 - - - +
89C VAL 3.2 0.2 - - - -
90C LEU* 1.3 74.4 - - + +
92C GLU* 1.3 62.1 + - - +
94C VAL* 3.3 10.0 + - + +
95C ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.5 15.4 - - + +
76C TRP* 2.8 32.2 + - + +
77C LYS* 3.0 28.3 + - - +
80C MET* 3.8 26.5 - - + -
88C GLN* 3.1 18.1 + - + +
89C VAL 3.1 8.7 + - - +
91C ARG* 1.3 75.2 - - - +
93C ILE* 1.3 61.0 + - - +
95C ALA* 3.7 6.0 - - - +
96C CYS* 2.8 32.9 + - - +
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 4.6 11.4 - - + -
42C LEU* 3.6 26.4 - - + +
89C VAL* 3.0 29.8 + - + +
90C LEU* 3.3 29.4 + - + +
92C GLU* 1.3 75.7 - - - +
94C VAL* 1.3 63.4 + - + +
96C CYS* 3.8 0.7 - - - +
97C THR* 2.8 37.6 + - + +
107C LEU* 4.5 15.0 - - + -
123C VAL* 4.3 26.9 - - + +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU 3.2 16.5 + - - +
91C ARG* 3.5 10.1 - - - +
92C GLU 3.2 0.2 - - - -
93C ILE* 1.3 78.7 - - + +
95C ALA* 1.3 64.0 + - - +
97C THR* 3.2 7.2 + - - -
98C LYS* 3.0 34.6 + - + +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 3.7 16.2 - - + -
77C LYS* 4.9 4.0 - - - +
91C ARG 2.9 16.3 + - - +
92C GLU* 3.2 13.4 + - - +
94C VAL* 1.3 78.6 - - - +
96C CYS* 1.3 61.8 + - - +
98C LYS* 3.4 8.0 + - - +
99C ALA* 3.1 24.6 + - - +
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Residues in contact with CYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.1 7.9 - - + -
43C GLU 5.3 0.2 - - - -
44C PHE* 4.2 11.9 - - - -
76C TRP* 3.7 47.2 - - + -
92C GLU 2.8 21.3 + - - +
93C ILE* 3.8 3.1 - - - +
95C ALA* 1.3 73.0 - - - +
97C THR* 1.3 56.8 + - - +
99C ALA* 3.2 3.6 + - - +
100C PHE* 2.9 29.2 + - - +
105C VAL* 3.8 32.3 - - + -
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 2.8 33.5 + - + +
94C VAL* 3.2 11.6 + - - -
96C CYS* 1.3 71.7 - - - +
98C LYS* 1.3 59.4 + - - +
100C PHE 4.2 4.9 - - - -
101C PRO* 3.1 31.7 - - - +
105C VAL* 4.1 14.1 - - + -
123C VAL* 5.1 1.8 - - + +
124C GLN* 3.2 40.8 - - + +
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 3.0 25.9 + - + +
95C ALA* 3.6 7.9 - - - +
96C CYS 3.3 0.2 - - - -
97C THR* 1.3 78.3 + - - +
99C ALA* 1.3 60.6 + - - +
101C PRO* 3.5 13.9 - - - +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 3.7 28.3 - - + -
95C ALA 3.1 16.6 + - - +
96C CYS 3.2 0.4 + - - +
98C LYS* 1.3 76.5 - - - +
100C PHE* 1.3 71.4 + - + +
101C PRO* 3.5 5.8 - - - +
140W VAL* 4.0 24.2 - - + +
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PHE* 3.5 47.6 - + + -
76C TRP* 3.9 13.2 - + - -
96C CYS* 2.9 13.9 + - - +
97C THR* 3.2 5.6 - - - +
99C ALA* 1.3 86.2 - - + +
101C PRO* 1.3 62.6 - - - +
102C ASP 3.2 3.5 + - - -
103C ALA* 3.2 22.1 + - + +
105C VAL* 4.6 2.1 - - + +
124C GLN* 2.9 19.4 + - - -
3W VAL* 4.5 2.2 - - + -
5W THR* 3.5 29.6 - - - -
6W PRO* 4.1 2.5 - - + -
7W VAL* 4.5 12.1 - - + -
140W VAL* 3.6 33.0 - - + -
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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
------------------------------------------------------------
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