Contacts of the strand formed by residues 241 - 250 (chain B) in PDB entry 3NNJ
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 ARG 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.6 12.4 - - + +
104B SER* 3.1 21.7 - - - -
105B VAL* 3.0 35.5 + - + +
106B GLU 4.5 1.1 - - - -
107B PRO 4.1 2.2 + - - -
109B HIS* 3.2 40.2 + - - -
111B GLY 4.8 2.2 - - - +
138B ASP* 4.3 2.9 - - - -
146B GLY 3.7 20.0 - - - +
230B SER* 4.0 21.8 + - - -
231B VAL 2.6 29.5 + - - -
232B PRO* 2.7 21.0 - - - +
233B LEU* 3.3 25.1 - - + +
240B LEU* 1.3 72.1 - - - +
242B ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 4.7 15.3 + - - +
37B LEU* 5.1 9.0 - - - +
38B ASP* 3.1 27.7 + - - -
102B LEU* 4.8 3.8 - - + -
103B PHE 3.7 3.4 - - - -
104B SER* 4.2 15.3 - - - -
136B PRO* 3.6 2.1 - - - +
137B LEU* 2.7 52.5 + - + +
138B ASP* 3.1 31.3 + - - +
239B LYS* 6.2 3.0 - - - +
240B LEU* 4.6 22.7 - - + +
241B ARG* 1.3 76.7 - - - +
243B ALA* 1.3 57.3 + - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.5 7.2 - - - +
103B PHE* 2.8 43.2 + - + +
134B TRP* 3.1 37.5 - - + +
135B ILE 3.0 13.0 - - - +
136B PRO* 3.8 4.5 - - + -
137B LEU* 4.0 2.5 - - - +
241B ARG 5.7 0.2 - - - -
242B ARG* 1.3 77.7 - - - +
244B PHE* 1.3 61.0 + - - +
245B VAL* 5.1 1.3 - - + -
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.5 22.2 - - + -
37B LEU* 3.4 43.3 - - + -
73B TYR* 3.8 22.2 - + + -
75B PHE* 4.2 1.1 - + - -
76B VAL* 3.4 38.1 - - + -
100B ASN* 4.6 2.9 - - + -
101B ALA 3.3 18.4 - - - -
102B LEU* 4.3 8.3 - - + -
133B ILE 3.5 1.7 - - - +
134B TRP* 3.6 0.7 - - - -
135B ILE* 2.7 58.4 + - + +
137B LEU* 3.9 19.3 - - + -
243B ALA* 1.3 74.5 - - - +
245B VAL* 1.3 62.4 + - - +
246B ILE* 4.2 4.3 - - + -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B HIS 3.7 2.1 - - - +
101B ALA* 2.7 44.0 + - + +
103B PHE* 4.2 24.2 - - + -
132B SER* 4.5 17.7 - - - +
133B ILE 3.4 7.0 - - - +
134B TRP* 4.0 19.7 - - + -
148B MSE 5.4 5.2 - - + -
222B PHE* 5.4 4.5 - - + -
243B ALA 4.6 0.2 - - - +
244B PHE* 1.3 79.4 - - - +
246B ILE* 1.3 66.1 + - - +
247B ARG* 4.0 10.1 + - + +
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 4.2 10.8 - - + -
80B ILE* 3.3 46.9 - - + -
97B ILE* 3.9 15.9 - - + -
99B HIS 3.4 4.3 - - - +
100B ASN* 3.5 28.0 - - + +
132B SER* 3.2 8.0 - - - -
133B ILE* 3.0 35.9 + - + +
135B ILE* 3.4 21.5 - - + -
244B PHE* 4.6 4.0 - - + -
245B VAL* 1.3 79.7 - - - +
247B ARG* 1.3 65.4 + - - +
248B LEU* 3.4 12.7 - - + +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.8 0.9 - - - -
98B MSE 2.8 39.0 + - + +
99B HIS* 3.0 48.1 + - - +
101B ALA* 5.6 3.0 - - - +
120B SER* 3.0 35.1 + - - +
121B PHE* 4.0 24.2 - - + -
123B PHE* 4.0 7.3 - - + -
131B ALA 3.6 3.8 - - - -
132B SER* 4.4 4.9 - - - +
245B VAL* 5.1 10.1 - - + -
246B ILE* 1.3 72.9 - - - +
248B LEU* 1.3 56.9 + - - +
283B ASP* 3.0 41.4 + - - -
285B VAL* 3.6 20.3 - - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 5.0 0.2 - - + -
84B LEU* 4.0 27.4 - - + -
87B LEU* 5.1 0.2 - - + -
95B LEU* 4.1 23.8 - - + -
96B MSE 3.4 6.3 - - - +
97B ILE* 4.2 18.8 - - + +
98B MSE 4.6 0.7 - - - -
121B PHE* 3.6 4.3 - - - -
130B GLY* 3.5 0.9 - - - -
131B ALA* 2.9 38.1 + - + +
132B SER* 4.1 3.6 - - - +
133B ILE* 3.5 28.0 - - + -
221B PHE* 4.3 9.0 - - + -
246B ILE* 3.4 21.8 - - + +
247B ARG* 1.3 77.5 - - - +
249B VAL* 1.3 77.1 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.3 9.6 - - - +
96B MSE 3.0 36.0 + - + +
98B MSE 3.9 30.7 - - + -
121B PHE* 4.8 1.1 - - + -
123B PHE* 4.3 7.9 - - + -
124B THR* 3.9 16.2 - - + -
129B PHE* 3.6 24.9 - - - +
130B GLY* 4.4 3.4 - - - -
248B LEU* 1.3 83.3 - - - +
250B ASP* 1.3 71.0 + - - +
253B THR* 3.6 19.5 - - + +
302B LEU* 4.3 7.4 - - + -
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Residues in contact with ASP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 3.4 16.9 - - + +
94B ASN* 2.8 36.1 + - - +
95B LEU* 4.6 0.7 - - - +
96B MSE 4.4 4.7 - - - +
129B PHE* 3.8 23.4 + - + -
249B VAL* 1.3 84.9 - - - +
251B TYR* 1.3 70.1 + - - +
252B ASP* 2.9 32.8 + - - +
253B THR* 3.0 27.3 + - - +
302B LEU* 6.0 0.5 - - - +
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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