Contacts of the strand formed by residues 304 - 314 (chain B) in PDB entry 5NJ8
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 VAL 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B LEU* 3.4 31.9 - - + -
266B ARG* 3.4 5.9 - - - -
267B MET* 2.9 38.1 + - + +
269B CYS* 4.8 11.4 - - - -
302B HIS 6.1 0.4 - - - +
303B PHE* 1.3 82.9 - - - +
305B VAL* 1.3 64.4 + - - +
306B VAL* 3.5 13.2 + - + -
343B LEU* 4.3 11.9 - - + -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.8 19.7 - - + -
265B CYS 3.8 5.2 - - - +
266B ARG* 4.8 10.1 - - + +
304B VAL* 1.3 73.6 - - - +
306B VAL* 1.3 60.4 + - - +
307B HIS 4.2 0.2 - - - -
343B LEU* 3.7 9.2 - - - +
344B GLN* 3.1 44.6 + - + +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 4.8 3.4 - - + -
196B VAL* 5.9 0.2 - - + -
197B LEU* 4.7 7.2 - - + -
264B ILE* 3.4 5.5 - - - +
265B CYS* 2.9 38.3 + - - +
267B MET* 3.6 46.7 - - + -
304B VAL* 3.5 14.8 + - + -
305B VAL* 1.3 76.8 - - - +
307B HIS* 1.3 63.5 + - - +
308B CYS* 3.6 22.7 + - - -
341B GLY* 4.0 11.7 - - - -
342B ARG 3.7 11.2 - - - +
343B LEU* 4.8 5.4 - - + -
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Residues in contact with HIS 307 (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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123A ASN* 4.5 3.6 + - - -
262B SER* 3.3 27.1 - - - -
263B PHE 3.0 11.5 + - - -
264B ILE* 3.6 15.2 - - + +
306B VAL* 1.3 71.4 - - - +
308B CYS* 1.3 68.7 + - - +
309B THR* 3.3 17.4 + - + +
340B ILE 3.9 0.9 - - - +
341B GLY* 3.3 0.7 - - - -
342B ARG* 2.9 70.9 + - + +
344B GLN* 3.1 36.5 - - + +
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Residues in contact with CYS 308 (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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177B PHE* 4.1 18.4 - - + -
261B ARG 5.3 0.2 - - - -
262B SER* 3.4 5.2 + - - -
263B PHE* 2.9 59.2 + - + +
265B CYS* 4.1 14.8 - - - -
267B MET* 3.9 17.3 - - - -
306B VAL* 3.6 25.8 - - - -
307B HIS* 1.3 70.9 + - - +
309B THR* 1.3 61.7 + - - +
339B ALA* 5.2 3.1 - - + -
340B ILE 3.5 5.8 - - - +
341B GLY* 4.2 2.9 - - - -
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Residues in contact with THR 309 (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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121A ALA 3.0 14.6 + - - +
122A LEU* 4.1 0.3 - - - -
123A ASN* 3.4 35.8 + - + +
260B ARG* 4.7 0.9 - - - -
261B ARG 4.3 4.3 - - - -
262B SER* 3.5 9.6 - - - +
307B HIS* 3.3 32.5 + - + +
308B CYS* 1.3 72.7 - - - +
310B GLY* 1.3 58.3 + - - +
339B ALA* 3.7 4.0 - - - -
340B ILE* 2.9 37.3 + - - +
342B ARG* 3.8 17.4 + - - +
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Residues in contact with GLY 310 (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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121A ALA* 3.2 13.9 + - - -
260B ARG* 3.2 22.8 - - - +
261B ARG 2.9 23.5 + - - +
262B SER* 5.2 0.2 - - - -
309B THR* 1.3 76.0 - - - +
311B TYR* 1.3 61.1 + - - -
337B LEU* 5.1 2.2 - - - -
338B VAL 3.4 12.1 - - - -
339B ALA* 3.5 7.8 - - - +
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Residues in contact with TYR 311 (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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117A PHE* 4.0 16.3 - + - -
120A GLN* 4.3 24.1 - - + +
121A ALA* 4.4 10.1 - - - -
259B SER 4.1 11.2 - - - +
260B ARG* 3.5 21.3 - - + +
261B ARG 4.7 0.7 - - - +
310B GLY* 1.3 74.5 - - - +
312B ILE* 1.3 76.9 + - - +
313B LYS* 3.6 28.0 + - + +
337B LEU* 3.8 5.2 - - - +
338B VAL* 2.9 61.9 + - + +
150D THR* 5.4 11.0 - - - -
151D ASP 6.1 0.7 - - - -
152D GLY* 4.7 20.8 - - - -
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Residues in contact with ILE 312 (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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181B CYS* 4.1 18.2 - - - -
224B GLN 5.2 0.4 - - - +
225B LEU* 6.3 0.4 - - - -
227B THR* 5.1 5.8 - - + -
259B SER* 3.4 23.5 + - - +
261B ARG* 3.2 42.8 - - + +
311B TYR* 1.3 84.7 - - - +
313B LYS* 1.3 63.7 + - - +
335B PHE* 3.8 27.8 - - + -
336B CYS 3.5 7.9 - - - +
337B LEU* 3.9 19.7 - - + -
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Residues in contact with LYS 313 (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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117A PHE* 4.6 17.6 - - + -
311B TYR* 3.6 33.3 + - + +
312B ILE* 1.3 74.4 - - - +
314B ALA* 1.3 76.4 + - - +
315B TRP* 3.6 7.2 + - + +
335B PHE* 4.4 3.1 - - - -
336B CYS* 2.8 33.6 + - - +
338B VAL* 4.1 11.0 - - + +
152D GLY* 5.0 8.1 - - - -
153D SER* 4.3 21.9 - - - -
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Residues in contact with ALA 314 (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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313B LYS* 1.3 91.5 - - - +
315B TRP* 1.3 71.2 + - - +
316B PRO* 4.1 7.2 - - + +
329B ALA* 5.4 7.4 - - + +
334B LYS 4.0 7.2 - - - +
335B PHE* 3.6 36.7 - - + +
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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