Contacts of the helix formed by residues 98 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.0 33.6 + - - +
94A ASN* 3.3 14.0 + - + +
95A THR 2.9 19.6 + - - -
96A PHE 3.2 0.2 - - - -
97A LYS* 1.3 75.7 - - + +
99A LEU* 1.3 62.7 + - - +
100A ASP 3.4 1.1 - - - -
101A SER* 2.9 30.5 + - - +
102A TRP* 3.0 16.2 + - - -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 5.6 0.2 - - - +
86A LEU* 3.9 38.1 - - + +
87A VAL 4.4 4.9 - - - +
88A PHE* 3.6 31.6 - - + +
95A THR 3.9 13.0 - - - +
96A PHE* 3.4 24.2 - - + +
97A LYS 3.2 2.4 - - - -
98A THR* 1.3 77.5 - - - +
100A ASP* 1.3 52.3 + - - +
102A TRP* 3.1 12.1 + - + +
103A ARG* 2.7 35.7 + - - +
122A VAL* 4.0 8.3 - - + -
142A TRP* 3.5 36.6 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS 4.4 6.6 + - - +
98A THR 3.4 0.2 - - - -
99A LEU* 1.3 78.5 - - - +
101A SER* 1.3 52.7 + - - +
103A ARG* 3.0 10.4 + - - +
104A ASP* 2.6 51.1 + - - +
142A TRP* 3.0 37.8 + - - -
146A LYS* 3.3 27.9 + - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS 5.1 0.8 + - - -
98A THR* 2.9 27.7 + - - +
100A ASP* 1.3 78.2 - - - +
102A TRP* 1.3 61.3 + - - +
104A ASP* 4.1 8.2 - - - +
105A GLU* 3.1 30.8 + - - +
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Residues in contact with TRP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.8 37.6 - - + +
15A GLY* 3.4 35.2 - - - -
16A ASP* 2.8 32.3 + - - +
64A THR* 5.8 2.0 - - - -
65A ALA 5.1 3.1 - - - -
66A GLY* 4.3 21.5 - - - -
71A GLN* 5.8 1.8 - - - -
78A TYR* 4.6 7.2 - - - -
86A LEU* 3.7 17.9 - - + -
98A THR* 3.0 31.1 + - - -
99A LEU* 3.4 11.9 - - + +
101A SER* 1.3 83.6 + - - +
103A ARG* 1.3 57.8 + - - +
105A GLU* 3.4 10.8 + - + +
106A PHE* 3.0 29.6 + - - +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.1 10.3 - - + +
99A LEU 2.7 20.1 + - - +
100A ASP* 3.4 17.3 - - - +
102A TRP* 1.3 73.8 - - - +
104A ASP* 1.3 66.9 + - - +
106A PHE* 3.4 3.1 + - - +
107A LEU* 3.1 32.6 + - + +
115A PRO 5.5 1.4 + - - -
116A GLU* 3.4 24.6 + - - +
118A PHE 5.3 1.2 + - - -
120A PHE* 3.5 53.4 - - + -
142A TRP* 4.8 8.1 - - + -
146A LYS* 3.6 42.7 + - - +
147A ASN* 3.8 17.6 - - - +
149A ILE* 4.4 6.9 - - - +
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASP* 2.6 35.8 + - - +
101A SER* 4.1 6.7 - - - +
103A ARG* 1.3 75.6 + - - +
105A GLU* 1.3 66.7 + - - +
107A LEU* 3.2 11.3 + - - +
108A ILE* 3.1 31.9 + - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 6.0 0.4 - - + -
75A VAL* 5.6 1.7 - - - +
78A TYR* 4.0 15.3 + - - +
101A SER 3.1 20.3 + - - +
102A TRP* 3.8 14.1 - - + +
103A ARG 3.4 0.2 - - - -
104A ASP* 1.3 75.4 - - - +
106A PHE* 1.3 63.9 + - - +
108A ILE* 3.3 10.6 + - - +
109A GLN* 2.9 58.5 + - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.5 4.9 - - + -
14A LEU* 3.6 19.9 - - + +
78A TYR* 3.5 29.8 - + + -
81A ALA* 3.7 22.0 - - + -
84A CYS* 3.9 17.7 - - + -
102A TRP 3.0 18.3 + - - +
103A ARG 3.7 4.0 - - - +
104A ASP 3.2 0.2 - - - -
105A GLU* 1.3 76.9 - - - +
107A LEU* 1.3 63.3 + - + +
109A GLN* 3.0 7.0 + - - +
110A ALA* 2.9 45.3 + - + +
112A PRO* 4.9 0.9 - - + -
118A PHE* 3.4 48.0 - + - -
120A PHE* 3.7 17.9 - + + -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.1 35.6 + - + +
104A ASP* 3.2 9.8 + - - +
106A PHE* 1.3 78.9 - - + +
108A ILE* 1.3 61.9 + - + +
111A SER* 3.1 29.4 - - - +
112A PRO* 4.3 13.9 - - + +
115A PRO* 3.5 38.1 - - + +
116A GLU* 4.1 17.9 - - - +
118A PHE* 4.6 1.6 - - + -
120A PHE* 3.9 21.8 - - + -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 5.4 0.2 + - - -
104A ASP* 3.1 22.3 + - + +
105A GLU* 3.6 11.2 - - - +
106A PHE 3.2 0.2 - - - -
107A LEU* 1.3 80.5 - - + +
109A GLN* 1.3 77.3 + - - +
111A SER* 3.7 12.6 + - - -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLY* 4.7 4.9 - - - -
75A VAL* 3.4 28.4 + - - +
76A ALA* 5.3 2.1 - - - +
78A TYR* 3.6 28.2 - - + -
79A ARG* 3.3 29.3 + - - -
105A GLU* 2.9 50.0 + - - +
106A PHE 3.0 3.5 + - - +
108A ILE* 1.3 91.9 - - - +
110A ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.2 3.4 - - + +
79A ARG* 4.1 38.7 + - - +
81A ALA* 5.0 1.6 - - + -
106A PHE* 2.9 40.7 + - + +
109A GLN* 1.3 77.4 - - - +
111A SER* 1.3 70.1 + - - +
112A PRO* 2.9 13.0 - - + +
118A PHE* 5.8 0.9 - - + -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.0 16.8 + - - -
107A LEU 3.1 19.4 + - - -
108A ILE* 3.7 11.7 + - - -
109A GLN 3.3 0.4 - - - -
110A ALA* 1.3 78.2 + - - +
112A PRO* 1.3 71.6 - - - +
113A ARG* 3.7 1.2 + - - -
115A PRO* 5.7 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