Contacts of the strand formed by residues 124 - 134 (chain D) in PDB entry 1L3C
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 LEU 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D ASP* 5.3 0.7 - - - -
101D ILE* 3.5 26.9 - - + +
102D ASP 4.2 2.2 - - - +
104D ALA* 4.8 1.1 - - + -
120D ILE* 3.2 14.4 + - + +
121D LYS* 3.5 12.6 + - - +
122D ASP 3.6 0.7 - - - +
123D LYS* 1.3 77.4 - - - +
125D LYS* 1.3 71.7 + - - +
126D PRO* 3.8 1.9 - - - +
128D GLY* 3.7 30.3 - - - +
129D ARG 4.2 14.1 - - - +
130D ILE* 4.0 23.1 - - + -
152D PHE* 4.1 23.1 - - + -
184D THR* 5.4 0.2 - - - +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN 5.5 0.2 + - - -
36D VAL* 4.0 13.1 - - - +
56D ARG* 4.6 8.3 - - - +
99D PRO* 6.2 0.4 - - - +
100D ASP* 3.7 39.6 + - + +
101D ILE 2.8 19.9 + - - +
102D ASP* 3.3 39.5 + - - +
123D LYS 3.3 0.2 + - - -
124D LEU* 1.3 79.4 - - - +
126D PRO* 1.3 79.2 - - + +
128D GLY* 2.9 15.5 + - - +
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Residues in contact with PRO 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASP* 5.2 2.4 - - - +
124D LEU 4.3 2.5 - - - +
125D LYS* 1.3 93.0 - - + +
127D GLY* 1.3 59.3 + - - +
128D GLY 3.4 0.2 + - - -
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS 3.3 0.4 + - - -
126D PRO* 1.3 73.1 - - - +
128D GLY* 1.3 62.4 + - - +
129D ARG* 3.0 28.0 + - - +
186D VAL* 4.4 21.0 - - - +
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASP* 3.0 19.1 - - - -
124D LEU* 3.7 21.8 - - - +
125D LYS 2.9 17.4 + - - -
126D PRO 3.2 0.6 - - - -
127D GLY* 1.3 83.6 - - - +
129D ARG* 1.3 62.4 + - - +
152D PHE* 5.7 0.7 - - - -
184D THR* 4.4 1.4 + - - -
185D GLY 3.9 11.8 - - - +
186D VAL 5.2 0.2 - - - -
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Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU 4.0 8.7 - - - +
29D ALA* 2.6 45.4 + - - +
30D GLU* 3.0 33.0 + - - +
35D ASP* 3.6 19.8 + - - -
102D ASP* 2.9 31.2 + - - +
103D ILE* 3.5 10.6 - - - +
104D ALA* 2.9 26.9 + - - +
124D LEU* 4.2 2.3 - - - +
127D GLY 3.0 25.6 + - - +
128D GLY* 1.3 76.1 - - - +
130D ILE* 1.3 66.5 + - - +
131D ILE* 5.1 5.4 - - + -
184D THR* 4.1 7.6 - - - +
185D GLY 4.6 1.1 - - - +
186D VAL* 3.9 24.5 - - + +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA* 3.3 12.3 - - + +
106D VAL* 4.8 3.4 - - + -
117D LEU* 4.2 23.6 - - + +
120D ILE* 3.7 26.9 - - + -
121D LYS* 5.0 4.0 - - - +
124D LEU* 4.0 15.0 - - + -
129D ARG* 1.3 77.4 - - - +
131D ILE* 1.3 68.9 + - - +
132D VAL* 4.3 11.0 - - + -
147D LEU* 4.2 13.0 - - + -
152D PHE* 3.8 32.1 - - + -
182D ILE 4.5 0.4 - - - -
183D TYR* 3.3 4.5 - - - +
184D THR* 3.1 39.0 + - + +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.9 35.2 - - + +
28D LEU* 4.1 11.7 - - + +
29D ALA* 3.7 41.3 - - + +
103D ILE* 5.0 3.1 - - + -
104D ALA 2.9 9.2 + - - +
105D VAL* 3.3 15.6 - - + +
106D VAL* 2.8 25.6 + - - +
129D ARG* 5.1 5.2 - - + -
130D ILE* 1.3 79.7 - - - +
132D VAL* 1.3 70.4 + - - +
133D THR* 5.1 0.9 - - - +
181D LEU* 4.5 14.1 - - + -
182D ILE 3.5 6.1 - - - +
183D TYR* 4.2 12.6 - - + -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 3.5 14.4 - - + +
107D GLY 5.4 0.7 - - - +
109D SER* 6.1 0.2 - - - -
113D LEU* 4.4 14.4 - - + -
117D LEU* 4.2 27.4 - - + -
130D ILE* 4.4 6.7 - - + -
131D ILE* 1.3 77.1 - - - +
133D THR* 1.3 71.1 + - - +
134D ALA 3.8 0.8 + - - +
139D THR* 4.4 8.5 - - + -
143D ALA* 4.1 24.0 - - + -
147D LEU* 4.5 11.4 - - + -
180D ALA 3.5 1.2 - - - +
181D LEU* 3.4 7.3 - - - -
182D ILE* 2.8 42.5 + - + +
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Residues in contact with THR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 5.3 11.1 - - + +
25D ILE* 4.0 22.3 - - - +
47D VAL* 5.8 0.3 - - - +
105D VAL* 4.7 6.6 - - - +
106D VAL 2.9 15.4 + - - +
107D GLY* 3.6 29.1 - - - +
131D ILE* 5.2 0.3 - - - +
132D VAL* 1.3 75.7 - - - +
134D ALA* 1.3 62.5 + - - +
135D ILE* 4.3 10.1 + - + +
139D THR* 4.4 4.0 - - - +
179D VAL* 4.3 16.8 - - + -
180D ALA 3.7 4.3 - - - -
181D LEU* 4.0 6.1 - - - +
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 5.1 0.2 - - + -
133D THR* 1.3 74.8 - - - +
135D ILE* 1.3 67.5 + - - +
136D LEU 4.5 0.2 - - - -
139D THR* 3.8 23.6 - - + -
140D LYS* 3.6 32.5 - - + +
179D VAL* 3.8 1.9 - - - +
180D ALA* 2.9 32.8 + - + +
182D ILE* 3.9 16.4 - - + -
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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