Contacts of the helix formed by residues 93 - 108 (chain C) in PDB entry 1L9W
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 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C ILE* 1.3 75.8 - - - +
94C THR* 1.3 65.3 + - - +
95C GLN* 3.4 22.4 - - + +
96C HIS* 2.9 32.2 + - - +
97C TYR* 3.0 23.5 + - - +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS* 5.3 5.0 + - - -
92C ILE 4.1 0.4 + - - -
93C THR* 1.3 72.2 - - - +
95C GLN* 1.3 84.3 + - - +
97C TYR* 3.2 10.0 + - - +
98C LEU* 2.9 28.3 + - + +
119C THR* 3.7 35.3 + - + +
123C ASP* 4.0 19.5 - - - +
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Residues in contact with GLN 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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93C THR* 3.4 20.4 - - + +
94C THR* 1.3 103.8 + - - +
96C HIS* 1.3 59.4 + - - +
98C LEU* 3.4 8.1 + - - +
99C THR* 3.1 24.7 + - - -
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Residues in contact with HIS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 3.0 26.8 + - + -
56C ALA* 3.7 20.5 - - + +
58C THR* 4.9 7.0 - - - -
92C ILE* 4.1 27.1 - - + -
93C THR* 2.9 27.2 + - - +
95C GLN* 1.3 75.0 - - - +
97C TYR* 1.3 51.9 + - - +
99C THR* 3.3 12.7 + - + +
100C LEU* 2.8 50.3 + - + +
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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
----------------------------------------------------------
81C PHE* 3.5 44.6 + + + -
83C SER* 5.5 4.0 - - - -
92C ILE* 3.6 15.6 - - + +
93C THR 3.0 15.9 + - - +
94C THR* 3.5 9.0 - - - +
96C HIS* 1.3 71.5 - - - +
98C LEU* 1.3 75.0 + - + +
100C LEU* 3.2 4.7 + - - +
101C ASN* 3.0 50.9 + - - -
114C ASP 3.8 3.5 + - - -
115C LEU* 3.4 18.7 - - + -
116C GLU* 2.9 39.6 + - + +
119C THR* 3.6 29.6 - - + -
124C VAL* 6.0 0.2 - - + -
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Residues in contact with LEU 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 THR* 2.9 24.8 + - + +
95C GLN* 3.7 6.5 - - - +
97C TYR* 1.3 91.0 - - + +
99C THR* 1.3 60.9 + - - +
101C ASN* 3.2 4.5 + - - +
102C ARG* 2.8 43.5 + - - +
115C LEU* 5.3 3.4 - - + -
119C THR* 4.8 3.8 - - + -
123C ASP* 3.6 41.7 - - + +
124C VAL* 5.8 1.3 - - + -
127C THR* 3.4 31.4 - - + +
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Residues in contact with THR 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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58C THR* 4.7 14.1 - - + +
95C GLN 3.1 15.4 + - - -
96C HIS* 3.3 19.2 + - + +
98C LEU* 1.3 76.0 - - - +
100C LEU* 1.3 62.4 + - - +
102C ARG* 3.3 7.0 + - - +
103C ALA* 2.9 24.1 + - + +
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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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49C VAL* 4.6 8.5 - - + -
55C ILE* 3.9 23.3 - - + +
58C THR* 4.6 13.5 - - + +
61C VAL* 4.7 15.0 - - + -
79C PHE* 4.0 15.6 - - + -
81C PHE* 4.2 22.4 - - + -
92C ILE* 4.0 21.3 - - + -
96C HIS* 2.8 47.6 + - + +
97C TYR* 3.2 5.1 + - - +
99C THR* 1.3 73.5 - - - +
101C ASN* 1.3 59.9 + - - +
103C ALA* 3.4 6.4 + - - +
104C ALA* 3.0 27.0 + - - +
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Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 3.4 28.0 - - - +
81C PHE* 5.0 4.8 + - - +
97C TYR* 3.0 55.4 + - - +
98C LEU* 3.8 5.2 - - - +
100C LEU* 1.3 77.1 - - - +
102C ARG* 1.3 63.2 + - - +
104C ALA* 3.4 3.7 + - - +
105C ILE* 3.0 29.4 + - - +
113C ILE* 3.7 26.5 - - + +
114C ASP 4.1 5.6 + - - +
115C LEU* 4.2 15.3 - - + +
127C THR* 4.7 5.6 - - + -
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Residues in contact with ARG 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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98C LEU* 2.8 34.2 + - - +
99C THR* 3.9 5.8 - - - +
101C ASN* 1.3 72.3 - - - +
103C ALA* 1.3 57.4 + - - +
105C ILE* 3.3 11.5 + - + +
106C ASP* 2.9 36.1 + - - +
126C ALA* 4.3 13.9 + - - +
127C THR* 4.6 16.9 + - + +
130C TYR* 3.6 62.6 - - + +
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Residues in contact with ALA 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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58C THR* 3.6 31.6 - - + -
62C LEU* 4.1 11.6 - - + +
99C THR* 2.9 19.0 + - + +
100C LEU 3.6 5.8 - - - +
101C ASN 3.3 0.2 - - - -
102C ARG* 1.3 76.8 - - - +
104C ALA* 1.4 56.4 + - - +
106C ASP* 3.2 9.9 + - - +
107C SER* 2.8 29.6 + - - -
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 4.4 8.1 - - + +
79C PHE* 3.9 38.4 - - + -
100C LEU 3.0 13.0 + - - +
101C ASN 3.7 7.2 - - - +
103C ALA* 1.4 70.8 - - - +
105C ILE* 1.3 68.3 + - - +
107C SER* 2.6 27.2 + - - -
108C GLY 3.7 1.2 + - - -
110C VAL* 3.7 22.7 - - + +
113C ILE* 4.6 1.8 - - + -
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Residues in contact with ILE 105 (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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101C ASN 3.0 22.8 + - - +
102C ARG* 3.6 6.5 - - - +
104C ALA* 1.3 79.0 - - - +
106C ASP* 1.3 62.8 + - - +
107C SER 3.3 0.2 + - - -
108C GLY* 3.3 9.9 + - - -
110C VAL* 4.7 1.1 - - - -
113C ILE* 4.0 27.4 - - + -
127C THR* 4.5 8.5 - - + +
130C TYR* 4.0 29.2 - - + +
131C ALA* 3.9 21.3 - - + +
134C HIS* 3.6 33.4 - - + +
136C VAL* 3.9 28.9 - - + +
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Residues in contact with ASP 106 (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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102C ARG* 2.9 20.1 + - - +
103C ALA* 3.6 10.6 - - - +
104C ALA 3.2 0.2 - - - -
105C ILE* 1.3 72.9 - - - +
107C SER* 1.3 66.1 + - - +
108C GLY* 3.2 1.0 + - - -
130C TYR* 2.6 33.4 + - - -
134C HIS* 4.4 11.0 + - - -
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Residues in contact with SER 107 (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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62C LEU* 4.0 16.9 - - - +
103C ALA 2.8 14.2 + - - -
104C ALA* 2.6 23.4 + - - +
106C ASP* 1.3 77.2 - - - +
108C GLY* 1.3 58.0 + - - +
109C LEU* 2.8 49.1 + - - +
110C VAL* 4.3 1.2 + - - +
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Residues in contact with GLY 108 (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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69C ARG* 5.2 2.3 + - - -
104C ALA 3.7 0.6 + - - -
105C ILE 3.3 10.0 + - - -
106C ASP 3.2 5.2 + - - -
107C SER* 1.3 77.0 + - - +
109C LEU* 1.3 64.8 + - - +
110C VAL 3.5 7.1 + - - +
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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