Contacts of the strand formed by residues 138 - 149 (chain D) in PDB entry 1N13
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 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D ALA* 3.9 8.5 - - + -
97D ILE 3.8 7.6 - - - +
99D LYS* 3.5 16.4 - - - +
128D LYS* 4.8 17.3 - - + -
131D PHE* 3.8 22.0 - - + -
136D TRP 3.6 1.2 + - - -
137D GLU* 1.3 76.8 - - - +
139D ASP* 1.3 62.5 + - - +
140D ARG* 3.7 27.4 - - - +
141D ILE* 3.8 32.1 - - + -
7008D MRD 4.6 12.7 - - + +
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Residues in contact with ASP 139 (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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97D ILE* 2.8 21.1 + - + +
98D PRO 3.7 13.5 - - - +
99D LYS* 3.7 33.4 + - + +
101D LYS* 3.4 19.3 + - - -
138D LEU* 1.3 76.1 - - - +
140D ARG* 1.3 94.5 + - - +
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Residues in contact with ARG 140 (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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60D GLU* 5.6 3.6 + - - -
61D ILE* 4.7 5.1 - - - +
95D VAL 3.9 0.3 - - - +
97D ILE* 2.9 56.1 + - + +
101D LYS* 5.0 2.8 - - - +
138D LEU* 3.7 7.6 - - - +
139D ASP* 1.3 108.2 + - - +
141D ILE* 1.3 68.7 - - - +
142D GLU* 2.8 36.3 + - + -
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Residues in contact with ILE 141 (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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94D SER* 4.1 17.0 - - - -
95D VAL 3.4 11.0 - - - +
96D ALA* 4.1 5.6 - - - -
124D ARG* 2.9 74.1 + - + +
127D ALA* 4.4 2.7 - - + -
128D LYS* 3.9 21.5 - - + +
138D LEU* 3.8 29.8 - - + +
140D ARG* 1.3 81.7 - - - +
142D GLU* 1.3 69.9 + - - +
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Residues in contact with GLU 142 (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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20C LEU* 3.7 8.8 - - + +
61D ILE* 3.5 42.4 - - + +
94D SER* 3.2 3.3 - - - -
95D VAL* 2.9 35.0 + - + +
97D ILE* 4.5 1.1 - - + -
124D ARG* 4.2 0.2 - - - +
140D ARG* 2.8 44.1 + - - +
141D ILE* 1.3 75.3 - - - +
143D SER* 1.3 62.5 + - - +
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Residues in contact with SER 143 (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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20C LEU* 4.0 3.7 - - - +
93D ILE 3.1 16.2 - - - -
94D SER* 3.8 4.9 - - - -
120D GLU* 2.7 31.6 + - - +
123D VAL* 4.4 1.6 - - - -
124D ARG* 2.9 39.8 + - - +
142D GLU* 1.3 77.7 - - - +
144D ILE* 1.3 73.1 + - - +
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Residues in contact with ILE 144 (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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20C LEU* 3.3 18.6 - - + +
21C VAL* 3.2 47.1 - - - +
22C ALA* 3.7 9.6 - - + +
92D ALA* 3.4 3.0 - - - +
93D ILE* 2.9 43.5 + - + +
120D GLU* 4.0 6.3 - - - -
143D SER* 1.3 86.7 - - - +
145D ALA* 1.3 62.0 + - - +
158D ALA* 4.6 0.2 - - - +
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Residues in contact with ALA 145 (chain D).
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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22C ALA* 4.5 7.0 - - - +
91D ALA 3.3 12.3 - - - +
92D ALA* 3.6 12.6 - - + +
116D LYS* 3.2 52.6 + - + +
119D ALA* 4.6 0.9 - - + -
120D GLU* 3.9 14.5 + - + +
144D ILE* 1.3 78.2 - - - +
146D VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 146 (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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22C ALA* 4.0 10.3 - - + -
23C GLY* 3.6 27.6 - - - +
24C SER* 4.2 7.2 - - - +
40C ASN* 5.5 0.9 - - - +
90D SER* 3.1 6.7 - - - -
91D ALA 3.0 37.6 + - - +
116D LYS* 4.2 7.9 - - - +
145D ALA* 1.3 77.9 - - - +
147D GLU* 1.3 72.3 + - - +
156D ALA* 4.4 3.3 - - + +
157D PHE 3.4 33.0 - - - +
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Residues in contact with GLU 147 (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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24C SER* 3.9 4.2 + - - -
88D THR* 3.8 13.4 - - + +
89D ILE 3.2 6.1 - - - +
90D SER* 3.1 16.8 - - - +
115D SER* 3.7 11.3 - - - -
116D LYS* 3.2 38.5 + - + +
146D VAL* 1.3 85.7 - - - +
148D HIS* 1.3 64.4 + - - +
149D THR* 6.0 1.3 - - - +
156D ALA* 5.1 0.7 - - - -
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Residues in contact with HIS 148 (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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24C SER* 3.1 31.3 + - - -
25C SER* 3.8 22.2 - - - -
26C GLU* 2.8 34.2 + - + +
87D GLU 3.5 1.0 - - - +
88D THR* 3.4 4.0 - - - -
89D ILE* 2.7 47.6 + - + +
147D GLU* 1.3 76.9 - - - +
149D THR* 1.3 76.7 + - - +
150D VAL* 3.8 5.4 - - + -
151D GLU* 5.5 0.9 - - - -
154D GLY* 3.9 18.2 - - - -
155D CYS 4.4 4.7 - - - +
156D ALA* 4.5 1.6 - - + -
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Residues in contact with THR 149 (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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26C GLU* 4.0 0.3 - - - +
86D GLY* 4.1 25.6 - - - +
87D GLU 3.5 3.6 - - - +
88D THR* 3.6 16.5 + - - +
147D GLU* 6.0 1.4 - - - +
148D HIS* 1.3 83.1 + - - +
150D VAL* 1.3 68.2 - - - +
151D GLU* 3.5 11.0 + - + +
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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