Contacts of the strand formed by residues 370 - 375 (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 LEU 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.5 4.9 - - + -
327A LYS* 3.6 21.7 + - - -
346A ILE* 3.9 14.8 - - + -
347A LYS 3.4 14.7 - - - +
348A GLU* 2.7 14.7 + - - +
350A THR 3.6 37.0 - - - +
351A ILE* 3.7 22.2 - - + -
366A VAL* 3.9 19.7 - - + -
369A ARG* 1.3 74.7 - - - +
371A PHE* 1.3 59.0 + - - +
372A SER 5.4 1.1 - - - +
381A PHE* 4.4 22.9 - - + -
382A ILE 3.9 6.3 - - - +
383A ALA* 4.0 17.5 - - + -
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Residues in contact with PHE 371 (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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27A ILE* 3.4 56.1 - - + -
28A ILE* 3.3 25.1 - - - -
29A SER* 3.9 9.2 - - - -
30A THR* 3.9 17.9 - - + -
327A LYS* 4.0 13.7 + - - +
328A TRP* 3.8 27.3 - + - +
346A ILE* 3.7 12.9 - - - +
369A ARG 4.9 0.2 - - - +
370A LEU* 1.3 75.6 - - - +
372A SER* 1.3 71.3 + - - +
382A ILE 2.8 17.5 + - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 2.8 26.7 + - - +
328A TRP* 3.3 34.5 - - - -
346A ILE* 4.1 4.2 - - - +
370A LEU* 5.4 1.6 - - - +
371A PHE* 1.3 85.2 - - - +
373A VAL* 1.3 67.3 + - - +
374A MET* 4.0 1.8 - - - +
381A PHE* 3.6 4.5 - - - +
382A ILE* 3.1 41.2 + - - +
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Residues in contact with VAL 373 (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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328A TRP* 3.1 27.0 + - + +
330A ASP* 3.3 13.3 - - + +
344A TYR* 3.9 29.2 - - + +
345A PHE* 4.4 0.9 - - - -
346A ILE* 3.3 47.6 - - + +
372A SER* 1.3 75.0 - - - +
374A MET* 1.3 62.9 + - - +
375A VAL* 4.6 11.2 - - + -
379A PRO* 4.8 1.1 - - + -
380A LEU 3.4 7.0 - - - +
381A PHE* 3.5 28.3 - - + -
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Residues in contact with MET 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.5 35.2 - - - +
31A TYR* 4.0 9.0 - - - -
32A LEU* 3.7 25.2 - - + +
37A LEU* 4.0 15.9 - - + -
230A HIS* 5.6 0.4 - - - +
328A TRP* 3.3 29.8 - - + +
330A ASP* 3.2 8.1 - - - +
372A SER* 4.0 13.2 - - - +
373A VAL* 1.3 76.6 - - - +
375A VAL* 1.3 61.7 + - - +
380A LEU* 3.1 39.2 + - - +
382A ILE* 4.0 6.1 - - + -
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Residues in contact with VAL 375 (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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32A LEU* 4.2 8.2 - - - +
330A ASP* 3.0 39.8 + - + +
331A ILE 4.2 8.7 - - - +
332A LYS* 3.7 36.1 - - + -
344A TYR* 4.6 11.4 - - + -
373A VAL* 4.6 4.0 - - + -
374A MET* 1.3 72.4 - - - +
376A THR* 1.3 69.9 + - - +
378A LYS 3.8 16.8 - - - -
379A PRO* 4.1 19.5 - - + -
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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