Contacts of the strand formed by residues 296 - 302 (chain B) in PDB entry 3N9V
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ARG 2.9 3.7 + - - +
267B PHE* 3.4 49.0 - - + -
268B PHE* 2.8 29.6 + - - +
294B PRO* 3.9 2.5 - - - +
295B ASP* 1.3 89.4 - - + +
297B TYR* 1.3 64.2 + - - +
298B CYS* 4.1 3.1 - - - -
351B LEU* 3.6 23.6 - - + -
352B TYR 3.4 10.5 - - - +
353B VAL* 3.9 15.3 - - + -
357B HIS* 5.3 0.2 - - + -
387B PHE* 4.6 4.3 - - + -
389B PHE* 4.5 14.4 - - + -
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Residues in contact with TYR 297 (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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268B PHE* 3.5 34.1 - + + -
287B LEU* 2.6 34.8 + - + -
294B PRO* 3.4 21.8 - - + +
296B VAL* 1.3 72.8 - - - +
298B CYS* 1.3 60.0 + - - +
299B VAL* 4.1 7.4 - - + -
330B LEU* 3.5 31.2 - - + -
331B HIS* 3.2 16.2 + - - +
336B TYR* 3.5 46.4 - + - -
350B LEU 3.7 0.7 - - - +
351B LEU* 3.3 6.8 - - - +
352B TYR* 2.7 56.9 + - + +
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Residues in contact with CYS 298 (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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267B PHE* 4.3 13.5 - - - -
268B PHE 2.9 18.1 + - - +
269B ALA* 3.4 6.8 - - + -
270B GLY 3.0 24.8 + - - +
296B VAL* 4.1 9.9 - - - -
297B TYR* 1.3 76.9 - - - +
299B VAL* 1.3 62.2 + - - +
349B LEU* 4.4 2.9 - - + -
350B LEU 3.4 7.0 - - - +
351B LEU* 3.7 19.5 - - + -
396B VAL* 4.0 36.1 - - + -
443B LEU* 4.4 6.3 - - + -
445B LEU* 4.3 3.2 - - + +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 4.6 2.9 - - + -
270B GLY 3.8 1.8 - - - +
286B TRP* 3.2 39.9 - - + -
287B LEU* 3.9 19.3 - - + -
297B TYR* 4.3 19.5 - - + -
298B CYS* 1.3 80.2 - - - +
300B GLY* 1.3 58.1 + - - +
301B PHE* 4.0 15.9 + - + -
326B VAL* 4.3 19.5 - - + -
348B MET 3.9 0.7 - - - +
349B LEU* 3.3 6.2 - - - +
350B LEU* 2.9 43.6 + - + +
352B TYR* 4.9 2.7 - - + -
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Residues in contact with GLY 300 (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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270B GLY 2.9 16.0 + - - -
271B THR* 3.1 5.5 - - - -
272B TYR* 2.8 25.9 + - - +
286B TRP* 4.3 1.9 - - - -
299B VAL* 1.3 74.6 - - - +
301B PHE* 1.3 66.8 + - - -
302B GLN* 4.2 1.8 - - - -
348B MET 3.3 6.7 - - - -
349B LEU* 3.8 2.9 - - - +
398B ASN* 3.7 4.9 - - - -
445B LEU* 3.7 13.9 - - - -
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Residues in contact with PHE 301 (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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272B TYR* 3.1 10.8 - + + +
274B VAL* 3.6 21.1 - - + -
286B TRP* 3.9 24.5 - + - -
299B VAL* 4.0 10.1 - - + -
300B GLY* 1.3 75.7 - - - -
302B GLN* 1.3 68.5 + - - +
304B LEU* 3.4 22.9 - - + -
322B TRP* 3.5 29.4 - + + -
326B VAL* 3.4 33.2 - - + -
346B GLY 3.9 1.3 - - - -
347B ILE* 3.7 1.6 - - - -
348B MET* 2.8 51.2 + - + +
350B LEU* 4.3 4.9 - - + -
398B ASN* 2.9 18.7 + - - -
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Residues in contact with GLN 302 (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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271B THR* 3.0 23.6 + - - -
272B TYR 3.0 8.2 + - - -
273B ASN* 3.4 27.1 + - - +
274B VAL* 3.0 24.4 + - - +
301B PHE* 1.3 83.1 + - - +
303B GLU* 1.3 70.0 + - - +
304B LEU 3.3 2.8 + - - -
346B GLY 3.2 6.1 - - - -
347B ILE* 4.6 2.0 - - + +
398B ASN* 2.8 27.8 + - - +
399B SER 4.8 0.2 - - - -
400B HIS* 3.7 40.4 - - + +
446B GLY* 3.3 6.1 - - - -
447B ASP* 3.5 20.0 - - + +
524B ASP* 4.4 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
------------------------------------------------------------
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