Contacts of the strand formed by residues 88 - 98 (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 THR 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D GLY 3.7 5.5 + - - -
87D GLU* 1.3 76.3 - - - +
89D ILE* 1.3 61.6 + - - +
113D LYS* 3.5 9.9 - - - +
114D CYS 3.5 36.2 + - - +
115D SER* 4.6 1.6 - - - -
147D GLU* 3.8 27.1 - - + +
148D HIS 3.4 8.3 - - - +
149D THR* 3.6 17.5 + - - +
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Residues in contact with ILE 89 (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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80D ILE* 3.6 44.0 - - + +
82D SER* 3.8 22.0 - - - +
87D GLU* 3.9 13.7 - - + +
88D THR* 1.3 77.1 - - - +
90D SER* 1.3 62.4 + - - +
112D GLY 3.6 3.8 - - - -
113D LYS* 4.5 2.0 - - + -
147D GLU* 3.2 2.4 - - - +
148D HIS* 2.7 51.2 + - + +
150D VAL* 4.1 10.8 - - + -
154D GLY 3.5 31.9 - - - +
155D CYS 4.0 0.7 - - - +
156D ALA* 3.7 12.2 - - + +
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Residues in contact with SER 90 (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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80D ILE* 3.5 4.0 - - - +
89D ILE* 1.3 71.8 - - - +
91D ALA* 1.3 61.7 + - - +
111D GLU* 3.2 2.8 - - - -
112D GLY 2.9 34.2 + - - -
114D CYS* 2.7 25.3 + - - -
115D SER 3.2 16.6 - - - -
116D LYS* 4.2 0.7 - - - -
119D ALA* 3.8 13.0 - - - +
146D VAL 3.1 11.2 - - - -
147D GLU* 3.1 21.7 - - - +
156D ALA* 3.9 4.9 - - - -
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Residues in contact with ALA 91 (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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78D GLY 3.8 9.9 - - - +
90D SER* 1.3 76.0 - - - +
92D ALA* 1.3 62.0 + - - +
110D TYR 3.2 9.2 - - - +
111D GLU* 4.5 2.9 - - + -
119D ALA* 4.5 2.4 - - - +
145D ALA* 3.3 2.6 - - - +
146D VAL* 3.0 31.1 + - + +
156D ALA* 3.7 23.3 - - - +
157D PHE* 3.7 12.3 - - - +
158D ALA* 3.7 16.2 - - - +
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Residues in contact with ALA 92 (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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78D GLY* 5.3 0.3 - - - -
91D ALA* 1.3 77.3 - - - +
93D ILE* 1.3 62.6 + - - +
109D GLU* 3.4 4.5 - - - +
110D TYR* 2.8 31.9 + - + +
119D ALA* 3.5 30.0 - - + +
120D GLU 4.0 0.2 - - - +
123D VAL* 3.7 12.3 - - + -
144D ILE 3.4 12.6 - - - +
145D ALA* 3.6 13.0 - - + -
158D ALA* 3.5 6.9 - - - +
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Residues in contact with ILE 93 (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 10.8 - - + -
76D ALA 3.7 23.3 - - - +
92D ALA* 1.3 74.6 - - - +
94D SER* 1.3 63.1 + - - +
107D ILE* 3.8 16.2 - - + -
108D MET 3.3 15.3 - - - +
109D GLU* 3.8 15.9 - - + -
123D VAL* 4.0 2.2 - - - +
143D SER* 3.1 5.9 - - - -
144D ILE* 2.9 55.0 + - + +
158D ALA* 4.0 8.3 - - + +
159D ALA* 3.8 28.9 - - - +
160D ALA* 3.8 11.4 - - + +
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Residues in contact with SER 94 (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* 4.9 1.8 - - - -
93D ILE* 1.3 78.7 - - - +
95D VAL* 1.3 62.9 + - - +
106D LEU 4.3 0.4 - - - -
107D ILE* 3.2 8.8 - - - +
108D MET* 2.9 33.5 + - - +
123D VAL* 2.8 40.9 + - - +
124D ARG* 4.2 0.2 - - - -
127D ALA* 3.4 10.2 - - - +
141D ILE* 4.1 11.4 - - - -
142D GLU 3.2 10.5 - - - -
143D SER* 3.8 5.6 - - - -
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Residues in contact with VAL 95 (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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18C VAL* 5.3 3.1 - - + -
20C LEU* 4.0 17.0 - - + -
55D MET* 4.1 28.5 - - + -
61D ILE* 3.3 28.0 - - + -
94D SER* 1.3 77.6 - - - +
96D ALA* 1.3 69.7 + - - +
97D ILE* 3.6 6.0 + - + +
106D LEU 3.2 9.4 - - - +
107D ILE* 4.1 16.8 - - + -
140D ARG 3.9 0.2 - - - +
141D ILE* 3.4 4.1 - - - -
142D GLU* 2.9 39.9 + - + +
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Residues in contact with ALA 96 (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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95D VAL* 1.3 72.1 - - - +
97D ILE* 1.3 59.8 - - - +
105D GLY* 3.1 8.1 - - - -
106D LEU* 2.8 32.1 + - + +
127D ALA* 3.9 24.9 - - + +
131D PHE* 3.4 28.7 - - + -
138D LEU* 3.9 14.1 - - + -
140D ARG 3.7 4.9 - - - -
141D ILE* 4.1 5.8 - - + -
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Residues in contact with ILE 97 (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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55D MET* 4.2 16.8 - - + -
61D ILE* 3.3 32.1 - - + -
95D VAL* 4.1 5.8 - - + +
96D ALA* 1.3 75.1 - - - +
98D PRO* 1.3 75.8 - - + +
101D LYS* 3.8 15.5 - - + +
105D GLY* 4.7 0.4 - - - -
131D PHE* 3.8 1.8 - - - -
138D LEU* 3.8 3.3 - - - +
139D ASP* 2.8 31.7 + - + +
140D ARG* 2.9 57.8 + - + +
142D GLU* 4.1 2.0 - - + +
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Residues in contact with PRO 98 (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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55D MET* 4.8 3.6 - - + -
96D ALA 4.0 1.3 - - - +
97D ILE* 1.3 90.7 - - + +
99D LYS* 1.3 64.9 + - - +
100D ASP 3.4 20.9 - - - +
101D LYS* 3.2 25.2 + - + +
103D LEU* 3.7 24.9 - - + +
104D CYS 3.5 24.2 - - - +
105D GLY* 4.0 4.9 - - - +
131D PHE* 3.5 17.4 - - + -
136D TRP* 4.9 0.7 - - + -
137D GLU 3.5 9.9 - - - +
139D ASP* 3.7 1.3 - - - +
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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