Contacts of the helix formed by residues 91 - 98 (chain C) in PDB entry 3EXF
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 ALA 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C THR* 3.8 15.7 - - + -
88C ALA 4.3 3.4 - - - +
89C TYR 3.1 5.7 + - - -
90C ARG* 1.3 74.3 - - - +
92C HIS* 1.3 60.5 + - - +
93C GLY 3.2 2.9 - - - -
94C PHE* 3.3 9.1 + - - -
95C THR* 2.3 42.2 + - + +
123C SER 5.3 1.5 + - - +
126C MET* 4.6 5.2 - - + -
131C PHE* 3.7 25.1 - - + -
134C GLY* 4.3 12.8 - - - +
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Residues in contact with HIS 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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45C MET* 3.4 23.4 - - + +
46C GLU* 3.3 31.6 + - - +
49C ALA* 5.3 0.2 - - - +
62C CYS* 4.2 10.8 - - - -
63C HIS 3.4 24.4 + - - +
64C LEU* 4.8 2.6 - - - +
65C CYS* 4.7 0.8 - - - -
89C TYR 5.2 0.6 + - - -
90C ARG 3.4 2.8 - - - -
91C ALA* 1.3 81.7 - - - +
93C GLY* 1.3 62.7 + - - +
95C THR* 3.7 5.4 + - - +
96C PHE 3.5 10.4 + - - -
105C ILE* 4.4 7.8 - - + +
109C LEU* 3.6 30.2 - - + +
123C SER* 3.4 36.4 + - - -
126C MET* 3.5 24.0 - - + -
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Residues in contact with GLY 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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42C VAL* 4.1 17.4 - - - +
45C MET* 4.8 0.4 - - - -
65C CYS* 3.4 23.5 - - - -
72C CYS* 4.2 13.2 - - - -
90C ARG 4.7 0.6 + - - -
91C ALA 3.2 0.4 - - - -
92C HIS* 1.3 78.8 - - - +
94C PHE* 1.3 64.4 + - - +
95C THR 3.3 0.2 + - - -
96C PHE* 3.5 3.3 + - - +
97C THR* 3.0 26.3 + - - +
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Residues in contact with PHE 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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65C CYS* 6.1 3.1 - - + -
68C GLN 6.0 0.4 - - - -
71C CYS* 4.8 3.4 - - + -
72C CYS* 3.6 30.7 - - + -
75C LEU* 3.6 26.0 - - + -
85C LEU* 3.8 24.5 - - + -
87C THR* 4.1 16.4 - - + -
90C ARG 4.4 8.3 - - - -
91C ALA* 3.3 10.8 + - - +
93C GLY* 1.3 78.9 - - - +
95C THR* 1.3 52.6 + - - +
97C THR* 3.1 8.1 + - - -
98C ARG* 2.8 41.7 + - + +
131C PHE* 3.8 21.8 - - + -
164C LEU* 3.4 25.1 - - + -
194C GLU* 4.0 18.4 - - - -
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Residues in contact with THR 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 ALA 2.3 36.1 - - - +
92C HIS 3.7 3.8 - - - +
94C PHE* 1.3 71.2 - - - +
96C PHE* 1.3 64.3 + - - +
98C ARG* 3.3 5.5 + - - +
99C GLY 3.3 5.4 + - - -
100C LEU* 2.9 37.5 + - - +
105C ILE* 3.1 25.3 - - - +
126C MET* 3.7 22.5 - - + +
128C ALA* 5.0 0.2 - - - +
131C PHE* 3.6 29.6 - - + -
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Residues in contact with PHE 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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37C ARG* 6.6 0.2 - - + -
38C MET* 4.1 28.7 - - + -
41C THR* 3.6 36.6 - - + -
42C VAL* 4.3 8.3 - - + -
45C MET* 4.0 13.0 - - + -
92C HIS 3.5 2.4 + - - -
93C GLY 3.5 7.5 + - - +
94C PHE 3.4 0.2 - - - -
95C THR* 1.3 76.3 + - - +
97C THR* 1.3 64.8 + - + +
98C ARG 2.7 15.6 + - - -
99C GLY* 2.8 16.1 + - - -
100C LEU 3.6 21.3 + - - +
101C SER* 5.3 0.9 - - - -
102C VAL* 3.6 25.6 - - + -
105C ILE* 3.6 10.1 - - + +
316C GLU* 5.7 2.7 - - - -
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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
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38C MET* 3.6 32.7 - - + +
42C VAL* 4.8 2.0 - - + -
72C CYS* 3.8 40.5 + - + +
73C VAL* 4.0 6.1 - - + -
76C GLU* 2.8 37.7 + - - +
85C LEU* 6.1 0.2 - - - +
93C GLY 3.0 19.1 + - - +
94C PHE* 3.1 21.3 + - - -
96C PHE* 1.3 75.2 - - + +
98C ARG* 1.3 53.3 + - - +
99C GLY 3.5 0.8 + - - -
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Residues in contact with ARG 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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76C GLU* 2.6 32.2 + - - -
79C ILE* 3.7 11.2 - - - +
80C ASN 3.1 26.7 + - - -
81C PRO* 3.3 13.4 + - - +
83C ASP 3.3 16.0 + - - -
85C LEU* 4.1 28.3 - - - +
94C PHE 2.8 20.3 + - - +
95C THR* 3.6 8.7 - - - +
96C PHE 2.7 2.6 + - - -
97C THR* 1.3 76.7 - - - +
99C GLY* 1.3 57.6 + - - +
100C LEU 3.7 0.4 - - - -
128C ALA* 4.1 12.3 - - + +
129C LYS* 4.0 12.1 + - - +
130C ASN* 3.1 31.1 + - - +
131C PHE* 3.5 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