Contacts of the helix formed by residues 86 - 99 (chain C) in PDB entry 1U5T
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 SER 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A GLN* 5.4 1.5 + - - -
14C TYR 4.5 3.0 + - - -
15C THR* 5.9 1.5 - - - +
16C ARG* 4.5 21.4 + - - -
84C SER 3.6 3.7 + - - -
85C VAL* 1.3 79.7 - - - +
87C GLN* 1.3 67.1 + - - +
88C VAL* 3.5 12.0 + - - +
89C PHE* 3.2 21.7 + - - +
90C ILE* 3.1 14.6 + - - +
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Residues in contact with GLN 87 (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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48C VAL* 2.6 51.3 + - - +
85C VAL 3.4 2.4 + - - -
86C SER* 1.3 66.5 - - - +
88C VAL* 1.3 57.6 + - + +
89C PHE 2.5 18.9 + - - -
90C ILE* 2.8 28.8 + - + +
91C ASP* 2.9 22.2 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 6.0 2.7 - - - +
86C SER* 3.6 10.1 - - - +
87C GLN* 1.3 77.6 - - + +
89C PHE* 1.3 55.3 + - - +
91C ASP* 3.2 27.1 - - - +
92C GLU* 3.6 7.5 + - - +
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Residues in contact with PHE 89 (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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13C LEU 5.0 0.4 - - - -
15C THR 6.0 0.7 - - - -
16C ARG* 3.1 38.6 - - + +
23C ARG* 3.9 10.3 - - + -
26C GLN* 3.8 28.3 - - + -
27C ILE* 4.2 17.7 - - + -
30C TRP* 4.1 12.6 - + - -
85C VAL* 3.7 13.2 - - + -
86C SER* 3.2 19.7 + - - +
87C GLN 2.5 5.9 + - - -
88C VAL* 1.3 73.3 - - - +
90C ILE* 1.3 69.0 + - - +
91C ASP 2.6 2.7 + - - -
92C GLU* 2.7 28.7 + - + +
93C ILE* 2.7 53.7 + - + -
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Residues in contact with ILE 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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48C VAL* 3.6 16.4 - - + +
76C PHE* 2.9 37.9 - - + -
85C VAL* 3.3 34.3 - - + +
86C SER 3.3 16.2 - - - +
87C GLN* 2.8 28.2 + - + +
89C PHE* 1.3 76.1 - - - +
91C ASP* 1.3 51.2 + - - +
93C ILE* 2.9 12.9 + - - +
94C TRP* 2.5 65.2 + - + +
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Residues in contact with ASP 91 (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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48C VAL* 3.8 12.6 - - - +
87C GLN* 2.9 26.1 - - - +
88C VAL* 3.2 16.8 - - - +
89C PHE 2.6 2.2 + - - -
90C ILE* 1.3 74.4 - - - +
92C GLU* 1.3 58.7 + - - +
94C TRP* 2.5 35.8 + - - +
95C SER* 2.8 12.3 + - - -
121C TYR* 5.6 0.3 + - - -
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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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23C ARG* 3.1 38.4 + - - -
27C ILE* 4.7 16.5 - - + +
88C VAL* 3.6 6.2 + - - +
89C PHE* 2.7 24.8 + - + +
91C ASP* 1.3 76.2 - - - +
93C ILE* 1.3 63.9 + - - +
95C SER* 3.5 8.4 - - - -
96C GLN* 3.2 20.2 + - + +
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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
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27C ILE* 4.1 23.1 - - + -
30C TRP* 3.2 46.0 - - + +
31C ILE* 4.5 19.1 - - + +
34C ILE* 5.5 3.4 - - + -
76C PHE* 5.0 15.0 - - + -
85C VAL* 4.7 2.0 - - + -
89C PHE* 2.7 39.7 + - + +
90C ILE* 3.0 16.6 - - + +
91C ASP 2.6 3.6 + - - -
92C GLU* 1.3 72.1 - - - +
94C TRP* 1.3 73.1 + - + +
95C SER 3.0 0.7 + - - -
96C GLN* 3.0 2.4 + - - +
97C MET* 2.8 23.2 + - + +
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Residues in contact with TRP 94 (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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34C ILE* 4.2 5.2 - - + -
46C MET* 3.1 38.6 - - + -
47C SER 3.4 23.6 + - - -
48C VAL* 3.6 13.2 - - + +
76C PHE* 3.9 11.1 - + - -
90C ILE* 2.5 41.1 + - + +
91C ASP* 2.5 15.8 + - - +
93C ILE* 1.3 73.5 - - + +
95C SER* 1.3 67.1 + - - +
97C MET* 2.9 51.6 + - + +
98C THR* 2.9 5.5 + - - -
103C CYS* 3.4 25.8 - - + -
121C TYR* 3.2 48.5 - + + +
123C ILE* 4.6 3.1 - - + -
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Residues in contact with SER 95 (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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91C ASP 2.8 12.9 + - - -
92C GLU* 3.5 13.7 - - - -
94C TRP* 1.3 66.0 - - - +
96C GLN* 1.3 53.3 + - - -
97C MET 2.5 4.3 + - - -
98C THR* 2.3 39.4 + - - +
99C LYS* 2.7 24.2 + - - +
121C TYR* 5.0 0.2 + - - -
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Residues in contact with GLN 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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27C ILE* 4.3 20.4 - - + -
28C SER* 5.6 1.3 - - - +
31C ILE* 3.4 8.8 - - + +
92C GLU* 3.2 12.7 + - + +
93C ILE 3.0 3.9 + - - +
95C SER* 1.3 79.7 + - - +
97C MET* 1.3 55.8 + - - +
98C THR 3.3 0.2 - - - -
99C LYS* 4.1 29.5 + - - +
100C GLU* 3.0 50.8 + - - +
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Residues in contact with MET 97 (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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31C ILE* 3.2 38.1 - - + +
34C ILE* 2.9 43.5 - - + -
35C SER* 4.6 2.5 - - - +
93C ILE* 2.8 13.8 + - + +
94C TRP* 2.9 33.2 - - + +
95C SER 2.5 5.3 + - - -
96C GLN* 1.3 75.6 - - - +
98C THR* 1.3 55.0 + - - -
100C GLU* 4.0 1.7 - - - +
101C GLY 3.4 2.9 + - - -
102C LYS* 3.1 44.9 + - - +
103C CYS* 3.2 27.7 + - + +
123C ILE* 4.9 4.7 - - + -
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Residues in contact with THR 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 TRP 2.9 3.2 + - - -
95C SER* 2.3 37.6 + - - +
97C MET* 1.3 67.9 - - - +
99C LYS* 1.3 72.3 + - + +
100C GLU 2.7 4.5 - - - -
101C GLY* 2.1 30.5 + - - +
103C CYS* 2.8 35.8 + - - -
104C LEU* 4.7 1.6 - - - +
105C PRO* 3.8 18.6 - - + +
112C ARG* 6.2 1.6 - - - +
121C TYR* 5.4 2.5 - - - -
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Residues in contact with LYS 99 (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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95C SER* 2.7 18.8 + - - +
96C GLN* 4.1 29.5 + - - +
98C THR* 1.3 82.8 - - + +
100C GLU* 1.3 60.0 + - - +
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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
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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