Contacts of the helix formed by residues 90 - 101 (chain C) in PDB entry 3CMM
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 LYS 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C ASP 4.1 6.5 - - - +
68C PRO* 3.5 34.5 - - + +
69C GLU 3.4 8.3 - - - -
70C PRO* 5.5 0.7 - - + -
88C GLY 3.9 1.0 + - - +
89C GLN* 1.3 72.2 - - - +
91C ARG* 1.3 65.7 + - - +
93C ASP* 3.3 35.2 + - - +
94C VAL* 3.2 18.9 - - - +
112C ASP* 5.6 6.7 + - - +
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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
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44C LEU* 3.9 19.3 - - + +
45C LYS* 3.9 22.3 - - - +
67C ASP* 2.7 44.3 + - + +
69C GLU* 2.8 42.1 + - - +
70C PRO 3.7 10.9 + - - -
71C VAL* 3.5 23.1 - - + +
75C ASP* 3.1 36.1 + - - -
82C LEU* 4.3 9.9 - - + -
89C GLN 3.6 0.4 + - - -
90C LYS* 1.3 69.2 - - - +
92C GLY* 1.3 65.0 + - - +
94C VAL* 3.6 1.5 + - - +
95C THR* 2.7 31.4 + - - +
131C THR* 3.7 15.8 + - - +
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Residues in contact with GLY 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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44C LEU* 4.3 3.8 - - - -
65C VAL* 4.0 21.9 - - - +
67C ASP* 2.8 28.2 + - - +
91C ARG* 1.3 72.8 - - - +
93C ASP* 1.3 63.1 + - - +
95C THR* 3.1 12.3 + - - -
96C ARG* 3.1 16.5 + - - +
110C VAL* 4.2 11.3 - - - +
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Residues in contact with ASP 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 GLN* 5.9 1.8 - - + -
90C LYS* 3.3 38.3 + - + +
92C GLY* 1.3 76.1 - - - +
94C VAL* 1.3 63.0 + - + +
95C THR 3.5 0.3 + - - -
96C ARG* 3.8 14.1 + - - +
97C ALA* 4.6 3.5 + - - +
110C VAL* 3.6 27.5 - - - +
112C ASP* 4.6 6.9 - - - +
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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
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71C VAL* 4.6 1.8 - - + -
81C PHE 4.6 2.7 - - - +
82C LEU* 3.3 33.0 - - + -
86C ASP* 3.8 29.8 - - + +
89C GLN* 3.4 32.1 - - + +
90C LYS 3.2 18.2 + - - +
91C ARG 4.0 3.8 - - - +
93C ASP* 1.3 77.2 - - + +
95C THR* 1.3 63.4 + - - +
97C ALA* 4.5 5.6 + - - +
98C LYS* 4.2 19.4 - - - +
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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
----------------------------------------------------------
44C LEU* 3.5 27.3 + - + +
49C VAL* 3.8 26.7 - - + -
79C GLN* 3.2 16.7 + - - +
81C PHE* 4.4 9.3 - - + +
82C LEU* 4.0 8.7 - - - +
91C ARG 2.7 21.6 + - - -
92C GLY 3.1 1.8 + - - -
94C VAL* 1.3 79.8 - - - +
96C ARG* 1.3 65.4 + - - +
97C ALA 3.3 1.1 - - - -
98C LYS* 3.1 6.5 + - - +
99C LEU* 3.0 28.8 + - + +
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Residues in contact with ARG 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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65C VAL* 5.3 3.8 - - + -
92C GLY 3.1 6.7 + - - +
93C ASP 3.9 10.8 - - - +
94C VAL 3.5 0.6 - - - -
95C THR* 1.3 77.5 - - - +
97C ALA* 1.3 73.8 + - - +
99C LEU* 3.3 5.5 + - - +
100C ALA* 2.9 55.8 + - - +
108C VAL* 3.1 43.7 + - + +
109C ASN* 4.8 0.7 - - - +
110C VAL* 3.6 35.7 - - + +
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Residues in contact with ALA 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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93C ASP 4.6 3.3 + - - +
94C VAL 4.5 6.2 + - - +
95C THR 3.3 0.6 - - - -
96C ARG* 1.3 102.1 - - + +
98C LYS* 1.3 63.2 + - + +
100C ALA* 3.4 3.8 + - - +
101C GLU* 3.4 29.3 + - - +
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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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80C PHE 5.6 0.8 + - - -
81C PHE* 3.6 72.0 + - + +
83C THR* 4.0 21.0 - - - +
86C ASP* 5.2 3.1 + - - -
94C VAL 4.2 13.0 - - - +
95C THR 3.1 8.3 + - - +
97C ALA* 1.3 80.1 - - + +
99C LEU* 1.3 63.1 + - - +
100C ALA 3.7 0.2 + - - -
101C GLU* 3.8 20.4 + - - +
102C LEU* 3.9 6.2 - - - +
486C ARG* 4.7 1.4 + - - -
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Residues in contact with LEU 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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44C LEU* 4.4 1.1 - - + -
49C VAL* 4.5 3.6 - - + -
52C ALA* 3.7 37.2 - - + +
53C LYS* 3.7 20.0 - - - +
56C VAL* 3.7 14.0 - - + +
63C MET* 5.0 2.5 - - + -
65C VAL* 4.0 21.1 - - + -
81C PHE* 4.0 14.8 - - + -
95C THR* 3.0 34.7 + - + +
96C ARG* 3.8 7.4 - - - +
98C LYS* 1.3 77.5 - - - +
100C ALA* 1.3 61.9 + - - +
102C LEU* 3.1 24.9 + - + +
108C VAL* 4.0 19.3 - - + -
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Residues in contact with ALA 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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96C ARG* 2.9 39.5 + - - +
97C ALA* 3.6 6.5 - - - +
98C LYS 3.3 0.4 - - - -
99C LEU* 1.3 76.7 - - - +
101C GLU* 1.3 59.5 + - + +
102C LEU 3.4 1.0 + - - -
103C ASN 3.7 18.2 + - - +
104C ALA* 4.1 6.2 + - - +
106C VAL 4.8 4.2 - - - +
108C VAL* 4.0 17.9 - - + +
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Residues in contact with GLU 101 (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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97C ALA* 3.4 18.4 + - - +
98C LYS* 4.0 13.7 - - - +
99C LEU 3.3 0.6 - - - -
100C ALA* 1.3 75.7 - - + +
102C LEU* 1.3 61.8 + - - +
103C ASN* 3.4 1.0 - - - -
104C ALA 5.2 1.0 + - - -
486C ARG* 3.5 45.6 + - + +
487C PRO* 5.1 6.6 - - - +
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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