Contacts of the helix formed by residues 96 - 107 (chain A) in PDB entry 1L2L
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ILE 3.8 0.8 + - - -
71A GLU* 2.8 42.9 + - - -
94A VAL* 3.4 2.0 - - - +
95A VAL* 1.3 79.3 - - - +
97A ARG* 1.3 64.1 + - - +
98A GLU* 3.4 18.0 + - - +
99A VAL* 3.2 16.4 + - - +
100A ARG* 3.0 27.1 + - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL 4.1 7.2 + - - -
96A SER* 1.3 72.0 + - - +
98A GLU* 1.3 58.6 + - - +
100A ARG* 3.0 20.5 + - - +
101A GLU* 2.9 45.1 + - + +
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Residues in contact with GLU 98 (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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71A GLU 5.8 0.7 - - - -
72A THR* 5.2 4.0 - - - +
73A ILE* 4.1 29.2 + - + +
96A SER* 3.2 10.7 + - - +
97A ARG* 1.3 80.3 - - - +
99A VAL* 1.3 59.4 + - - +
101A GLU* 3.3 13.4 + - - +
102A TYR* 3.0 25.3 + - - +
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Residues in contact with VAL 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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70A ILE* 3.9 16.4 - - + -
71A GLU* 3.4 13.2 - - - +
72A THR* 3.4 36.1 - - - +
73A ILE* 3.7 8.5 - - + +
76A LEU* 4.2 13.0 - - + -
94A VAL* 3.7 19.3 - - + -
96A SER* 3.2 13.0 + - - +
98A GLU* 1.3 77.3 - - + +
100A ARG* 1.3 61.6 + - - +
102A TYR* 3.3 7.7 + - + +
103A MET* 3.0 35.0 + - + +
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Residues in contact with ARG 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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93A LEU* 6.3 0.6 - - - +
94A VAL* 2.7 36.6 + - + -
95A VAL* 4.3 7.4 - - - +
96A SER 3.0 21.2 + - - +
97A ARG* 3.0 20.9 + - - +
99A VAL* 1.3 74.7 - - - +
101A GLU* 1.3 62.6 + - + +
103A MET* 3.3 8.6 + - - +
104A ARG* 2.8 30.2 + - - +
175A GLU* 4.0 18.6 + - - -
180A TYR* 4.3 3.8 + - + +
204A ALA 4.8 0.6 + - - -
205A ALA* 3.7 37.3 + - + +
206A ASP 4.0 10.1 - - - +
207A ASP* 4.4 23.2 + - - +
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Residues in contact with GLU 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 ARG* 2.9 30.5 + - + +
98A GLU* 3.5 11.4 + - - +
99A VAL 3.2 0.2 - - - -
100A ARG* 1.3 75.0 - - + +
102A TYR* 1.3 64.1 + - - +
104A ARG* 3.3 11.8 + - - +
105A LYS* 3.0 24.1 + - - +
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Residues in contact with TYR 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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50A ARG* 3.1 55.0 + - + +
54A VAL* 5.1 3.3 - - + +
73A ILE* 3.3 47.7 - - + +
76A LEU* 4.2 15.0 - - + -
77A LEU* 4.1 7.5 - - + +
98A GLU 3.0 13.6 + - - +
99A VAL* 3.4 13.0 - - + +
100A ARG 3.2 0.2 - - - -
101A GLU* 1.3 75.0 - - - +
103A MET* 1.3 63.9 + - + +
105A LYS* 3.1 11.4 + - - +
106A TRP* 2.8 45.8 + + - +
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Residues in contact with MET 103 (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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76A LEU* 4.0 22.2 - - + -
94A VAL* 3.6 29.8 - - + -
99A VAL* 3.0 27.8 + - + +
100A ARG* 3.6 6.7 - - - +
102A TYR* 1.3 77.7 - - + +
104A ARG* 1.3 61.9 + - - +
106A TRP* 3.2 9.6 + - - +
107A GLY 3.0 17.8 + - - +
180A TYR* 3.6 41.5 - - + -
182A TYR* 3.5 31.5 + - + +
203A GLY* 3.7 27.1 - - - -
205A ALA* 5.5 0.2 - - - -
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Residues in contact with ARG 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 ARG 2.8 20.0 + - - +
101A GLU* 3.5 12.3 - - - +
103A MET* 1.3 72.4 - - - +
105A LYS* 1.3 61.6 + - - +
107A GLY* 3.2 13.7 + - - -
108A TRP* 4.6 13.8 - - + -
176A ASP* 4.8 12.4 + - - -
178A ILE* 5.9 3.3 - - + +
180A TYR* 3.5 17.2 + - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ARG* 2.5 38.9 - - - +
101A GLU 3.0 14.1 + - - +
102A TYR* 3.5 12.6 - - - +
104A ARG* 1.3 71.7 - - - +
106A TRP* 1.3 69.4 + - - +
107A GLY* 3.0 3.9 + - - -
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Residues in contact with TRP 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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40A LYS* 2.7 45.4 + - - +
42A LEU* 3.9 25.6 - - + -
46A ASP* 2.9 27.5 + - - -
47A LEU* 4.1 11.0 - - + -
50A ARG* 3.2 43.8 + - - +
76A LEU* 3.7 10.5 - - + -
77A LEU* 3.7 30.7 - - + -
80A ILE* 5.1 3.8 - - + -
102A TYR* 2.8 28.2 + + - +
103A MET* 3.2 8.9 + - - +
105A LYS* 1.3 78.4 + - - +
107A GLY* 1.3 55.2 + - - +
108A TRP 4.1 0.2 + - - -
182A TYR* 3.5 36.1 - + - +
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Residues in contact with GLY 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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40A LYS* 3.3 18.0 - - - +
103A MET 3.0 12.4 + - - +
104A ARG 3.2 12.5 + - - -
105A LYS 3.0 5.0 - - - -
106A TRP* 1.3 79.5 - - - +
108A TRP* 1.3 74.8 + - - +
180A TYR* 4.5 7.1 - - - -
182A TYR* 5.1 1.6 - - - -
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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