Contacts of the helix formed by residues 98 - 111 (chain C) in PDB entry 3LAW
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 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ASP* 2.8 37.7 + - - +
94C ASN* 3.1 7.4 + - + +
95C THR 2.8 21.1 + - - -
96C PHE 3.0 0.2 + - - -
97C LYS* 1.3 75.9 - - + +
99C LEU* 1.3 65.5 + - - +
100C ASP 3.3 2.2 - - - -
101C SER* 2.7 33.6 + - - +
102C TRP* 3.1 13.5 + - - +
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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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14C LEU 5.4 0.2 - - - +
86C LEU* 3.7 40.9 - - + +
87C VAL 4.1 14.4 - - - +
88C PHE* 3.6 28.0 - - + -
95C THR 4.1 8.1 - - - +
96C PHE* 3.2 26.4 + - + +
97C LYS 3.4 0.2 - - - -
98C THR* 1.3 75.6 + - - +
100C ASP* 1.3 52.9 + - - +
102C TRP* 2.9 14.1 + - + +
103C ARG* 2.7 33.8 + - - +
122C VAL* 4.2 6.5 - - + -
142C TRP* 3.5 36.1 - - + -
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Residues in contact with ASP 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 PHE 5.1 0.2 + - - -
97C LYS 4.7 5.4 + - - +
98C THR 3.3 1.1 - - - -
99C LEU* 1.3 76.8 - - - +
101C SER* 1.3 54.8 + - - +
103C ARG* 3.2 7.6 + - - +
104C ASP* 2.7 64.2 + - - +
142C TRP* 3.5 18.3 + - + +
146C LYS* 2.7 39.9 + - - +
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Residues in contact with SER 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 LYS 5.0 1.6 + - - -
98C THR* 2.7 31.0 + - - +
100C ASP* 1.3 74.2 - - - +
102C TRP* 1.3 58.3 + - - -
104C ASP* 3.8 6.1 - - - +
105C GLU* 2.9 31.1 + - - +
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Residues in contact with TRP 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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14C LEU* 3.9 33.2 - - + +
15C GLY* 3.7 32.8 - - - -
16C ASP* 2.8 35.9 + - - +
64C THR* 5.9 0.7 - - - -
65C ALA 5.1 2.2 - - - -
66C GLY* 4.5 18.4 - - - -
71C GLN* 4.8 12.3 - - - -
78C TYR* 5.0 5.2 - - - -
86C LEU* 3.8 20.6 - - + -
95C THR 5.5 0.4 - - - -
98C THR* 3.1 33.7 + - + +
99C LEU* 2.9 13.4 + - + +
101C SER* 1.3 76.3 - - - +
103C ARG* 1.3 65.5 + - - +
105C GLU* 3.0 11.5 + - + +
106C PHE* 2.9 26.5 + - - +
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Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.2 10.8 - - + +
99C LEU 2.7 15.6 + - - +
100C ASP* 3.5 11.2 - - - +
102C TRP* 1.3 72.7 - - - +
104C ASP* 1.3 69.1 + - - +
106C PHE* 3.4 1.7 + - - +
107C LEU* 3.1 40.2 + - + +
115C PRO 4.7 3.6 + - - -
116C GLU* 3.5 30.3 + - - -
118C PHE 5.0 2.2 + - - -
120C PHE* 3.7 51.7 - - + -
142C TRP* 4.8 7.6 - - + -
146C LYS* 3.8 42.5 + - - +
147C ASN* 3.7 22.6 - - - +
149C ILE* 4.7 6.1 - - - +
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Residues in contact with ASP 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 ASP* 2.7 43.4 + - - +
101C SER* 3.9 5.6 - - - +
103C ARG* 1.3 77.8 + - - +
105C GLU* 1.3 61.0 + - - +
107C LEU* 3.5 13.1 + - - +
108C ILE* 3.2 28.6 + - + +
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Residues in contact with GLU 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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14C LEU* 6.0 0.2 - - + -
75C VAL* 5.5 2.4 - - - +
78C TYR* 4.2 14.0 + - - +
101C SER 2.9 19.5 + - - +
102C TRP* 3.0 17.0 + - + +
104C ASP* 1.3 73.4 - - - +
106C PHE* 1.3 55.2 + - - +
108C ILE* 3.0 7.3 + - - +
109C GLN* 2.8 75.0 + - + +
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Residues in contact with PHE 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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12C ILE* 3.7 26.0 - - + -
14C LEU* 3.8 13.0 - - + +
78C TYR* 3.7 26.9 - + - -
81C ALA* 3.8 15.0 - - + -
84C CYS* 3.7 18.2 - - + -
102C TRP 2.9 18.2 + - - +
103C ARG 3.9 2.2 - - - +
105C GLU* 1.3 72.6 - - - +
107C LEU* 1.3 66.6 + - + +
109C GLN 3.0 1.0 + - - -
110C ALA* 2.9 48.9 + - + +
112C PRO* 4.6 3.6 - - + -
118C PHE* 3.3 50.5 - + - -
120C PHE* 3.6 17.3 - + + -
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Residues in contact with LEU 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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103C ARG* 3.1 48.4 + - + +
104C ASP* 3.7 11.2 - - - +
106C PHE* 1.3 82.7 - - + +
108C ILE* 1.3 57.6 + - + +
111C SER* 3.1 24.8 + - - -
112C PRO* 3.8 24.4 - - + +
115C PRO* 3.6 30.2 - - + +
116C GLU* 4.3 9.4 - - - +
118C PHE* 4.8 0.7 - - + -
120C PHE* 3.7 21.1 - - + -
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Residues in contact with ILE 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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104C ASP* 3.2 16.2 + - + +
105C GLU* 3.0 12.2 + - - +
107C LEU* 1.3 77.1 - - + +
109C GLN* 1.3 82.0 + - - +
110C ALA 3.1 9.0 + - - -
111C SER* 3.6 12.0 + - - -
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Residues in contact with GLN 109 (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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75C VAL* 3.2 33.7 - - + +
78C TYR* 3.5 34.2 - - + +
79C ARG* 3.9 13.2 - - - +
105C GLU* 2.8 51.2 + - + +
106C PHE 3.0 0.2 + - - -
108C ILE* 1.3 93.2 - - - +
110C ALA* 1.3 57.8 + - - +
111C SER* 4.9 0.7 - - - -
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Residues in contact with ALA 110 (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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78C TYR* 3.9 26.0 - - + +
79C ARG* 4.1 20.9 + - - +
106C PHE* 2.9 34.9 + - + +
109C GLN* 1.3 78.3 - - - +
111C SER* 1.3 76.7 + - - +
112C PRO* 3.0 5.5 - - + +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG* 3.2 22.7 + - - -
107C LEU 3.1 11.6 + - - -
108C ILE 3.6 10.8 + - - -
109C GLN 4.9 0.3 - - - -
110C ALA* 1.3 81.8 + - - +
112C PRO* 1.3 71.9 - - - +
113C ARG 3.8 0.7 + - - -
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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