Contacts of the helix formed by residues 88 - 96 (chain C) in PDB entry 3UYS
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 88 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C GLY 3.8 1.4 + - - -
87C PRO* 1.3 77.3 - - - +
89C LEU* 1.3 60.8 + - - +
90C GLU* 3.3 9.5 + - - +
91C ASP* 3.0 37.8 + - - -
92C LEU* 3.0 27.1 + - - +
131C PRO 4.0 2.2 - - - -
132C ASP* 3.7 14.7 + - - -
134C PHE 3.2 12.1 - - - -
135C LEU* 3.7 18.7 - - - +
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Residues in contact with LEU 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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88C SER* 1.3 72.0 - - - +
90C GLU* 1.3 59.5 + - - +
92C LEU* 4.0 12.2 - - + +
93C PHE* 2.9 31.0 + - - +
100C PHE* 4.2 2.4 - - + -
108C LEU* 4.0 16.6 - - + -
112C MET* 3.9 26.7 - - + -
131C PRO* 3.3 11.5 + - + +
134C PHE* 2.8 35.4 + - + +
136C MET* 4.1 12.6 - - + -
145C VAL* 4.7 4.5 - - + -
206C PHE* 3.8 24.6 - - + -
290C TRP* 3.9 28.9 - - + -
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Residues in contact with GLU 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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88C SER* 3.1 1.9 + - - +
89C LEU* 1.3 78.3 - - - +
91C ASP* 1.3 62.7 + - - +
93C PHE* 3.5 5.1 + - - +
94C ASN* 2.9 36.9 + - - +
98C ARG* 3.6 15.9 + - - -
131C PRO* 3.4 30.3 + - + +
132C ASP* 3.3 33.9 - - - +
178C ARG* 4.9 2.4 + - - -
179C TYR* 4.2 3.3 + - - -
205C TYR* 3.1 32.6 + - - -
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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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87C PRO* 4.1 11.7 - - + +
88C SER* 3.0 35.8 + - - +
90C GLU* 1.3 76.8 - - - +
92C LEU* 1.3 60.4 + - - +
94C ASN* 3.3 9.9 + - - +
95C PHE* 3.0 30.4 + - + +
132C ASP* 4.7 4.7 - - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PRO* 3.9 25.8 - - + +
88C SER 3.0 20.8 + - - +
89C LEU* 4.0 7.6 - - + +
91C ASP* 1.3 75.7 - - - +
93C PHE* 1.3 63.9 + - - +
95C PHE* 3.1 10.0 + - + +
96C CYS* 3.1 29.3 + - - -
100C PHE* 3.8 2.0 - - - -
136C MET* 3.4 34.3 - - + -
290C TRP* 3.7 54.7 - - + +
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Residues in contact with PHE 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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89C LEU 2.9 20.9 + - - +
90C GLU* 3.7 7.4 - - - +
91C ASP 3.2 0.2 - - - -
92C LEU* 1.3 79.3 - - - +
94C ASN* 1.3 50.3 + - - +
96C CYS* 3.6 2.6 + - - +
98C ARG* 2.6 68.0 + - + -
99C LYS 3.3 20.0 + - - -
100C PHE* 3.3 30.3 - + + -
205C TYR* 3.5 61.2 - + - -
206C PHE* 3.7 26.5 - + + -
209C GLY* 3.8 11.0 - - - -
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Residues in contact with ASN 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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90C GLU* 2.9 31.9 + - - +
91C ASP* 3.3 10.5 + - - +
92C LEU 3.2 0.4 - - - -
93C PHE* 1.3 72.8 - - - +
95C PHE* 1.3 60.5 + - + +
96C CYS 2.9 11.1 + - - -
97C SER* 2.9 14.0 + - - -
98C ARG* 2.4 41.3 + - - +
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Residues in contact with PHE 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 3.0 15.0 + - - +
92C LEU* 3.1 17.2 + - + +
94C ASN* 1.3 76.3 - - + +
96C CYS* 1.3 60.7 + - - +
97C SER* 3.4 2.5 + - - -
290C TRP* 6.1 0.4 - - + -
293C LEU* 3.6 35.0 - - + +
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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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92C LEU 3.1 18.0 + - - +
93C PHE 4.0 3.6 - - - +
94C ASN 2.9 1.6 - - - -
95C PHE* 1.3 84.4 - - - +
97C SER* 1.3 70.8 + - - +
98C ARG 3.1 1.0 + - - -
99C LYS* 3.4 23.5 + - - +
100C PHE* 3.7 24.9 - - + -
289C ASP* 4.4 6.7 - - + -
290C TRP* 4.2 31.0 - - - -
293C LEU* 5.0 8.1 - - - -
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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