Contacts of the strand formed by residues 130 - 136 (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 GLY 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B PHE* 3.9 15.0 - - - -
124B THR* 5.7 0.2 - - - -
128B ASP 3.7 2.4 + - - -
129B PHE* 1.3 81.0 - - - +
131B ALA* 1.3 65.1 + - - +
223B ASN* 3.5 6.2 - - - +
224B LYS* 2.9 35.7 + - - +
248B LEU 3.5 10.8 - - - -
249B VAL* 4.4 0.9 - - - -
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Residues in contact with ALA 131 (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* 5.5 0.2 - - + -
121B PHE* 3.3 9.5 - - - -
129B PHE* 3.7 20.9 - - + -
130B GLY* 1.3 76.6 - - - +
132B SER* 1.3 69.0 + - - +
221B PHE* 3.8 18.8 - - + -
222B PHE 3.4 13.0 - - - +
223B ASN* 3.7 7.6 - - - +
224B LYS 4.1 2.0 - - - +
247B ARG* 3.6 0.3 - - - -
248B LEU* 2.9 35.4 + - + +
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Residues in contact with SER 132 (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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121B PHE* 3.5 18.5 - - - -
131B ALA* 1.3 80.8 + - - +
133B ILE* 1.3 63.9 + - - +
134B TRP 4.2 0.2 - - - -
221B PHE* 3.2 9.6 - - - -
222B PHE* 2.8 62.4 + - - -
245B VAL* 4.5 11.6 - - - +
246B ILE 3.2 9.8 + - - -
247B ARG* 4.4 5.4 - - - +
248B LEU* 4.1 0.4 - - - -
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Residues in contact with ILE 133 (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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24B ILE* 5.7 6.1 - - + -
25B PHE* 5.4 4.3 - - + -
80B ILE* 4.1 28.0 - - + -
83B LYS* 6.2 1.1 - - + -
87B LEU* 3.5 27.8 - - + -
132B SER* 1.3 80.0 - - - +
134B TRP* 1.3 60.5 + - - +
135B ILE* 3.7 15.5 + - + +
219B ALA* 3.8 25.6 - - + -
220B PHE 3.4 6.1 - - - +
221B PHE* 4.1 9.9 - - + -
244B PHE 3.5 2.1 - - - +
245B VAL* 3.4 5.5 - - - -
246B ILE* 3.0 34.3 + - + +
248B LEU* 3.5 18.8 - - + -
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Residues in contact with TRP 134 (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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103B PHE* 5.7 3.4 - + - -
132B SER 4.2 0.2 - - - -
133B ILE* 1.3 72.1 - - - +
135B ILE* 1.3 60.1 + - - +
136B PRO* 3.4 27.2 - - + +
140B ILE* 4.0 11.0 - - + -
146B GLY 5.0 1.6 - - - -
147B GLY* 3.9 32.1 - - - -
148B MSE 3.6 47.9 - - + +
214B TYR* 4.1 31.2 - + - -
219B ALA* 3.4 4.4 - - - -
220B PHE* 2.7 55.9 + - + +
222B PHE* 4.1 7.1 - - + -
243B ALA* 3.1 31.3 - - + +
244B PHE 3.6 1.1 - - - -
245B VAL* 4.0 16.8 - - + +
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Residues in contact with ILE 135 (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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25B PHE* 4.1 25.6 - - + -
30B ILE* 4.4 13.2 - - + -
33B ILE* 6.1 4.5 - - + -
76B VAL* 5.2 3.1 - - + -
80B ILE* 3.8 15.3 - - + -
133B ILE* 3.9 17.9 - - + +
134B TRP* 1.3 75.4 - - - +
136B PRO* 1.3 72.9 - - + +
137B LEU* 3.5 9.0 + - + +
218B ASP 4.4 5.4 - - - +
219B ALA* 4.3 3.6 - - + -
243B ALA* 3.0 4.5 - - - -
244B PHE* 2.7 51.2 + - + +
246B ILE* 3.4 32.8 - - + -
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Residues in contact with PRO 136 (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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30B ILE* 5.2 2.8 - - - +
134B TRP* 3.4 35.0 - - + +
135B ILE* 1.3 88.8 - - + +
137B LEU* 1.3 64.9 + - - +
138B ASP 4.0 15.0 - - - +
140B ILE* 4.3 5.2 - - + -
214B TYR* 4.0 22.0 - - + +
215B ASN 5.0 4.5 - - - +
216B LEU* 4.9 11.1 - - + +
217B GLY 5.1 1.6 + - - -
218B ASP 3.1 25.4 - - - +
219B ALA* 4.3 0.4 - - - -
242B ARG 3.6 7.0 - - - +
243B ALA* 3.8 5.8 - - + -
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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