Contacts of the helix formed by residues 89 - 104 (chain C) in PDB entry 3L9J
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 THR 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C PRO* 3.5 0.7 - - - +
88C GLN* 1.3 84.5 - - + +
90C GLY* 1.3 64.5 + - - +
91C SER* 3.3 7.5 + - - -
92C GLU* 3.1 32.9 + - + +
93C ASN* 3.0 20.3 + - - +
133C TYR* 3.7 14.5 - - - -
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Residues in contact with GLY 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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89C THR* 1.3 73.7 - - - +
91C SER* 1.3 57.3 + - - +
93C ASN* 3.3 2.8 + - - +
94C ASP* 2.9 34.5 + - - +
133C TYR* 3.4 25.9 - - - -
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Residues in contact with SER 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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89C THR* 3.2 7.2 + - - -
90C GLY* 1.3 72.4 - - - +
92C GLU* 1.3 66.0 + - - +
94C ASP* 3.4 13.8 + - - +
95C ALA* 3.0 23.4 + - - +
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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
----------------------------------------------------------
59C LYS* 4.0 24.0 + - - +
61C PHE* 5.3 1.4 - - - -
86C THR 4.0 3.1 - - - +
87C PRO* 3.7 12.8 - - + +
88C GLN* 2.9 35.9 + - - +
89C THR* 3.1 26.5 + - + +
91C SER* 1.3 77.2 - - - +
93C ASN* 1.3 62.7 + - - +
95C ALA* 3.3 7.6 + - - +
96C LEU* 3.0 23.4 + - - +
177C GLN* 5.9 0.9 + - - -
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Residues in contact with ASN 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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87C PRO* 3.2 28.8 - - + +
89C THR 3.0 7.9 + - - +
90C GLY 3.5 5.8 - - - +
91C SER 3.3 0.2 - - - -
92C GLU* 1.3 77.4 - - - +
94C ASP* 1.3 57.1 + - - +
96C LEU* 3.3 3.1 + - - +
97C TYR* 2.9 31.0 + - - +
133C TYR* 3.2 24.2 + - - +
135C ASN* 3.3 7.4 + - - -
155C LEU* 3.6 7.1 - - - +
161C GLY* 3.1 23.6 - - - +
163C TRP* 2.8 33.0 - - - +
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Residues in contact with ASP 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 GLY 2.9 19.9 + - - +
91C SER* 3.4 16.9 + - - +
93C ASN* 1.3 76.7 - - - +
95C ALA* 1.3 56.7 - - - +
97C TYR* 3.3 12.5 + - - +
98C GLU* 2.9 38.7 + - + +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LYS* 4.8 8.5 - - - +
61C PHE* 4.3 14.6 - - + -
91C SER 3.0 12.7 + - - +
92C GLU* 3.3 8.9 + - - +
94C ASP* 1.3 76.7 - - - +
96C LEU* 1.3 61.6 + - - +
98C GLU* 3.5 4.8 + - - +
99C TYR* 2.9 30.8 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 4.1 19.7 - - + -
85C SER* 3.7 26.9 - - - +
87C PRO* 3.7 28.0 - - + -
92C GLU 3.0 16.7 + - - +
93C ASN 3.7 4.5 - - - +
95C ALA* 1.3 77.0 - - - +
97C TYR* 1.3 56.3 - - - +
99C TYR* 3.3 3.7 + - - +
100C LEU* 2.8 29.9 + - - +
110C ILE* 4.1 12.3 - - + -
112C LEU* 3.9 15.5 - - + -
155C LEU* 4.1 6.7 - - + -
175C ILE* 3.8 37.7 - - + -
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Residues in contact with TYR 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 ASN* 2.9 18.2 + - - +
94C ASP* 3.3 13.2 + - - +
96C LEU* 1.3 76.1 - - - +
98C GLU* 1.3 78.1 + - + +
100C LEU* 3.3 2.6 + - + +
101C ARG* 3.0 63.4 + - + +
155C LEU* 4.1 13.4 - - + +
157C GLY* 3.4 27.1 + - - -
160C ASN* 3.0 40.2 + - + +
161C GLY* 3.6 26.7 - - - -
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Residues in contact with GLU 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 ASP* 2.9 24.6 + - + +
95C ALA* 3.9 4.7 - - - +
97C TYR* 1.3 96.0 - - + +
99C TYR* 1.3 64.2 + - - +
101C ARG* 3.6 20.1 + - - +
102C GLN* 3.3 37.5 + - - +
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Residues in contact with TYR 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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46C LEU 5.1 0.5 + - - -
47C GLN* 2.7 32.0 + - + -
49C VAL* 3.3 33.2 - - + -
61C PHE* 3.6 37.5 - + + -
62C LEU* 3.5 3.1 - - - +
63C ALA* 3.0 35.2 + - + +
95C ALA 2.9 18.1 + - - +
96C LEU 3.7 2.2 - - - +
98C GLU* 1.3 75.8 - - - +
100C LEU* 1.3 51.2 + - - +
102C GLN* 3.4 13.0 + - + +
103C SER* 2.8 58.7 + - - -
175C ILE* 3.8 18.4 - - + -
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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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96C LEU 2.8 16.3 + - - +
97C TYR 3.3 9.4 + - - +
99C TYR* 1.3 69.8 - - - +
101C ARG* 1.3 64.2 + - - +
103C SER* 3.8 6.1 - - - -
104C VAL* 2.8 30.0 + - + +
105C GLY 3.1 34.7 + - - +
108C ALA* 3.8 13.0 - - + +
110C ILE* 3.3 40.2 - - + -
155C LEU* 3.4 29.6 - - + +
157C GLY* 3.6 22.9 - - - +
175C ILE* 3.9 11.6 - - + +
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Residues in contact with ARG 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 TYR* 3.0 59.4 + - + +
98C GLU* 3.6 22.2 + - - +
99C TYR 3.5 0.2 - - - -
100C LEU* 1.3 77.7 - - + +
102C GLN* 1.3 64.3 + - + +
105C GLY* 3.4 25.8 + - - -
106C ASN* 3.3 53.3 + - - +
107C GLU* 5.0 4.4 + - - -
157C GLY 4.7 1.0 + - - -
160C ASN* 5.3 3.6 - - - +
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Residues in contact with GLN 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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49C VAL* 5.7 5.5 - - - +
98C GLU* 3.3 25.5 + - - +
99C TYR* 3.6 16.3 + - + +
100C LEU 3.3 0.4 - - - -
101C ARG* 1.3 81.0 - - + +
103C SER* 1.3 61.5 + - - +
105C GLY 4.9 0.3 + - - -
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Residues in contact with SER 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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46C LEU 5.3 10.8 + - - +
47C GLN 6.1 0.7 - - - -
63C ALA* 3.3 29.1 - - - +
65C THR* 4.3 9.9 - - - +
99C TYR* 2.8 50.1 + - - -
100C LEU* 3.7 1.7 + - - -
102C GLN* 1.3 74.2 - - - +
104C VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 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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63C ALA* 3.7 17.5 - - + -
64C PHE 5.0 1.3 - - - +
65C THR* 4.5 17.1 - - + +
100C LEU* 2.8 12.7 + - + +
102C GLN 5.3 0.2 - - - -
103C SER* 1.3 87.8 - - - +
105C GLY* 1.3 59.8 + - - +
108C ALA* 3.5 25.4 - - + +
110C ILE* 4.2 19.7 - - + -
173C PRO* 3.9 27.8 - - + -
174C TYR 5.1 0.2 - - - +
175C ILE* 4.7 2.9 - - + -
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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