Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 3NVN
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 TYR 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.9 25.7 - - + +
236A THR* 4.7 8.9 - - + +
241A ILE* 6.1 2.5 - - + -
243A TYR* 3.7 24.9 + + + -
331A ILE* 3.4 31.0 - - + -
332A LYS* 3.5 2.2 - - - -
333A GLU* 3.4 47.9 + - + -
334A LYS* 3.9 9.1 - - - +
339A ARG 3.7 17.3 - - - -
340A GLU* 1.3 76.6 - - - +
342A ARG* 1.3 63.6 + - - +
343A ILE* 4.1 1.6 - - + -
354A PHE 3.9 0.2 - - - +
355A ASP* 4.0 2.1 - - - -
356A THR* 2.9 46.5 + - + +
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 3.7 1.6 - - - -
332A LYS* 2.9 36.0 + - + +
333A GLU 5.7 0.2 - - - -
334A LYS* 3.9 23.7 - - + +
341A TYR* 1.3 76.3 - - - +
343A ILE* 1.3 62.2 + - - +
344A TYR* 3.8 33.7 + - + +
353A SER* 4.2 22.7 + - - -
354A PHE 3.5 7.2 - - - -
355A ASP* 3.0 32.5 + - - +
362A ARG* 3.5 29.6 - - - +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TYR* 4.8 4.3 - - + -
245A PHE* 5.2 0.2 - - + -
255A LEU* 4.1 16.2 - - + -
318A PRO* 4.3 6.7 - - + -
320A PHE* 3.9 23.1 - - + -
329A PHE* 4.2 12.3 - - + -
330A ASP 3.8 4.0 - - - +
331A ILE* 3.3 34.1 - - + -
341A TYR* 4.9 0.4 - - + -
342A ARG* 1.3 73.7 - - - +
344A TYR* 1.3 66.0 + - - +
345A PHE* 4.0 6.0 + - + -
352A TYR 3.9 0.2 - - - +
353A SER* 3.3 3.6 - - - -
354A PHE* 2.8 65.2 + - + +
356A THR* 4.0 17.5 - - + -
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Residues in contact with TYR 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A PHE* 3.1 4.3 - - - +
330A ASP 2.8 40.9 + - - +
332A LYS* 4.5 12.3 - - + -
342A ARG* 3.9 43.2 + - + +
343A ILE* 1.3 71.8 - - - +
345A PHE* 1.3 61.5 + - - +
351A ILE* 4.9 1.6 - - + -
352A TYR 3.4 15.9 - - - +
353A SER* 3.7 18.2 - - - -
373A VAL* 3.9 22.2 - - + +
375A VAL* 4.6 13.2 - - + -
379A PRO* 4.6 11.1 - - + +
381A PHE* 4.3 11.0 - + + -
391A ILE* 3.4 41.8 - - + +
394A MET* 5.0 2.2 - - - -
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 3.9 18.4 - + + -
320A PHE* 3.6 27.1 - + - -
322A GLY 3.9 23.6 - - - -
323A PRO* 3.9 8.7 - - + -
326A VAL* 3.7 20.6 - - + -
328A TRP 3.3 14.8 - - - +
329A PHE* 3.6 11.4 - - + -
343A ILE* 4.1 11.0 - - + -
344A TYR* 1.3 75.0 - - - +
346A ILE* 1.3 65.2 + - - +
352A TYR* 2.8 75.2 + + + +
353A SER 4.7 0.2 - - - -
354A PHE* 4.5 10.1 - - + -
361A THR* 4.5 10.1 - - + -
373A VAL* 4.5 0.7 - - - -
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A VAL* 3.4 8.1 - - - +
327A LYS* 3.3 57.7 + - + -
328A TRP* 3.2 12.5 + - + +
345A PHE* 1.3 78.1 - - - +
347A LYS* 1.3 72.5 + - - +
350A THR 3.5 11.9 - - - +
351A ILE* 4.0 7.6 - - - -
352A TYR* 4.3 2.2 - - - -
370A LEU* 3.9 20.2 - - + -
371A PHE 3.7 21.8 - - - +
372A SER* 4.1 3.6 - - - +
373A VAL* 3.3 32.1 - - + -
381A PHE* 4.1 14.1 - - + -
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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