Contacts of the helix formed by residues 89 - 104 (chain C) in PDB entry 3C3P
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ILE* 6.1 1.2 - - - +
87C ASP* 2.9 17.2 + - - +
88C PRO* 1.3 80.2 - - + +
90C ARG* 1.3 67.3 + - - +
91C ASP* 2.9 30.5 + - - +
92C ASN* 2.9 31.5 + - - +
93C VAL* 3.4 10.4 + - - +
113C VAL* 4.6 0.7 - - - -
211C EDO 5.3 1.7 + - - +
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Residues in contact with ARG 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 PRO 3.9 2.6 + - - +
89C ASP* 1.3 73.7 + - - +
91C ASP* 1.3 60.1 + - - +
93C VAL* 3.9 3.6 - - - +
94C GLU* 3.0 31.1 + - - +
113C VAL* 3.5 45.3 - - + +
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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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34C ARG* 4.0 25.5 + - - +
89C ASP* 2.9 21.7 + - - +
90C ARG* 1.3 78.8 - - - +
92C ASN* 1.3 60.5 + - - +
94C GLU* 4.0 5.5 - - - +
95C HIS* 3.2 27.0 + - - +
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Residues in contact with ASN 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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34C ARG* 5.3 0.3 + - - -
36C ILE* 4.2 8.1 - - - +
64C ASP 3.8 11.2 - - - +
65C GLY* 3.7 3.9 - - - -
66C LEU* 2.8 35.4 + - - +
67C GLY 4.2 5.2 + - - -
85C MSE 4.8 1.8 - - - -
87C ASP* 2.8 31.6 + - + +
89C ASP* 2.9 21.9 + - - +
91C ASP* 1.3 77.2 - - - +
93C VAL* 1.3 66.6 + - - +
95C HIS* 3.4 3.8 + - - +
96C ALA* 3.0 23.9 + - - +
211C EDO 3.1 24.5 + - - -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MSE 4.1 17.5 - - - -
87C ASP* 4.1 6.5 - - + -
89C ASP 3.4 8.1 + - - +
90C ARG* 3.9 5.4 - - - +
91C ASP 3.4 0.2 - - - -
92C ASN* 1.3 78.9 - - - +
94C GLU* 1.3 58.0 + - - +
96C ALA* 3.3 6.9 + - - +
97C ARG* 2.8 30.3 + - + +
111C LEU* 3.7 24.4 - - + +
112C GLN* 3.6 21.1 - - - +
113C VAL* 3.6 35.2 - - + +
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Residues in contact with GLU 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 ARG 3.0 18.4 + - - +
91C ASP* 4.2 6.7 - - - +
93C VAL* 1.3 76.1 - - - +
95C HIS* 1.3 63.9 + - - +
97C ARG* 2.9 40.6 + - - +
98C ARG* 2.9 70.5 + - - +
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Residues in contact with HIS 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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27C MSE 3.9 23.6 - - + -
30C ILE* 2.8 39.7 - - + +
34C ARG* 4.6 7.9 - - - +
66C LEU* 3.1 44.2 + - + +
91C ASP 3.2 19.7 + - - +
92C ASN 3.7 4.9 - - - +
93C VAL 3.3 0.2 - - - -
94C GLU* 1.3 78.2 - - - +
96C ALA* 1.3 62.3 + - - +
98C ARG* 3.4 9.0 + - + +
99C MSE 3.2 41.5 + - + +
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Residues in contact with ALA 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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66C LEU 4.3 0.4 + - - -
67C GLY* 3.8 11.0 - - - +
70C SER* 5.6 0.7 - - - -
85C MSE 3.6 24.5 - - + -
92C ASN 3.0 16.7 + - - +
93C VAL 3.5 4.9 - - - +
95C HIS* 1.3 76.3 - - - +
97C ARG* 1.3 66.0 + - - +
99C MSE 3.3 13.3 + - + +
100C LEU* 3.0 34.0 + - + +
111C LEU* 4.1 10.5 - - + -
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Residues in contact with ARG 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 VAL* 2.8 21.0 + - + +
94C GLU* 2.9 39.7 + - - +
96C ALA* 1.3 76.4 - - - +
98C ARG* 1.3 60.7 + - - +
100C LEU* 3.6 1.4 - - - +
101C HIS* 2.7 59.9 + - + +
106C ILE* 4.3 14.4 - - + +
111C LEU* 3.5 18.4 - - + +
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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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94C GLU* 2.9 51.8 + - - +
95C HIS* 3.7 9.0 - - + +
97C ARG* 1.3 85.4 - - - +
99C MSE 1.3 57.2 + - - +
101C HIS* 3.6 5.2 - - - +
102C ASP* 2.9 41.8 + - - +
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Residues in contact with MSE 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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23C VAL* 3.8 32.5 - - + +
27C MSE 3.7 22.4 - - - +
66C LEU 3.6 22.0 - - - +
67C GLY 3.7 17.0 - - - +
71C TRP* 3.8 24.2 - - + -
95C HIS* 3.2 26.0 + - + +
96C ALA* 3.8 13.7 - - + +
98C ARG* 1.3 78.8 - - + +
100C LEU* 1.3 61.9 + - + +
102C ASP* 3.3 8.2 + - - +
103C ASN* 2.9 33.4 + - - +
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Residues in contact with LEU 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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70C SER* 5.2 7.4 - - - -
71C TRP* 4.6 13.5 - - + +
74C ALA* 3.9 17.3 - - + -
96C ALA* 3.0 25.1 + - + +
97C ARG 3.8 2.2 - - - +
99C MSE 1.3 82.7 - - + +
101C HIS* 1.3 61.3 + - - +
103C ASN* 2.9 14.0 - - - +
104C GLY 2.8 23.0 + - - -
105C LEU* 2.9 30.9 + - + -
106C ILE* 3.1 24.0 + - + +
109C VAL* 3.7 33.7 - - + -
111C LEU* 4.4 6.3 - - + -
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Residues in contact with HIS 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 ARG* 2.7 35.7 + - + +
98C ARG* 3.6 7.0 - - - +
100C LEU* 1.3 77.6 - - - +
102C ASP* 1.3 74.1 + - - +
104C GLY* 3.0 14.6 + - - -
106C ILE* 4.0 21.7 - - + +
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Residues in contact with ASP 102 (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 VAL* 6.3 3.1 - - + -
98C ARG* 2.9 26.3 + - - +
99C MSE 3.6 7.4 - - - +
101C HIS* 1.3 90.9 + - - +
103C ASN* 1.3 58.7 + - + +
104C GLY 3.5 0.3 + - - -
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Residues in contact with ASN 103 (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 VAL* 5.7 8.3 - - + -
71C TRP* 3.4 30.9 - - - +
75C ARG* 5.0 1.8 - - - +
99C MSE 2.9 17.7 + - - +
100C LEU* 2.9 10.9 - - - +
102C ASP* 1.3 75.7 - - + +
104C GLY* 1.3 55.5 + - - +
105C LEU* 2.8 52.6 + - - +
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Residues in contact with GLY 104 (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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100C LEU 2.8 7.8 + - - -
101C HIS* 3.0 12.9 + - - -
102C ASP 3.2 0.6 + - - -
103C ASN* 1.3 77.2 - - - +
105C LEU* 1.3 56.1 + - - -
106C ILE* 2.9 17.3 + - - +
107C ASP* 3.3 20.9 + - - +
108C ARG* 6.0 0.2 - - - -
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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