Contacts of the strand formed by residues 350 - 354 (chain L) in PDB entry 6R90
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 350 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLN* 3.4 25.1 - - + +
94L PHE* 3.8 25.4 - - + -
95L LEU* 3.4 49.4 - - + -
98L LEU* 5.8 0.2 - - + -
344L TRP* 3.6 6.2 - - - -
345L HIS* 3.3 32.8 + - + +
348L TYR* 3.3 14.7 - - + -
349L ASN* 1.3 79.4 - - - +
351L ILE* 1.3 72.5 + - - +
374L VAL* 4.6 5.2 - - + -
375L PHE 3.2 17.3 - - - +
376L ASP* 4.3 4.3 - - + -
400L PHE* 6.1 3.4 - - + -
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Residues in contact with ILE 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304L LEU* 3.4 35.7 - - + -
312L ILE* 5.0 4.0 - - + -
314L VAL* 4.6 3.6 - - + -
327L ILE* 3.9 24.5 - - + -
342L ALA* 4.6 0.7 - - + -
343L ALA 3.5 14.1 - - - +
344L TRP* 4.1 22.7 - - + -
345L HIS* 4.9 0.9 - - - +
350L LEU* 1.3 81.0 - - - +
352L VAL* 1.3 64.2 + - - +
353L VAL* 3.7 23.1 - - + -
374L VAL* 3.3 7.1 - - - +
375L PHE* 2.9 42.6 + - + +
377L GLY* 4.3 11.2 - - - -
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Residues in contact with VAL 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341L LYS 4.9 0.7 - - - +
342L ALA* 4.0 0.7 - - - -
343L ALA* 3.1 33.7 + - + +
344L TRP 4.7 1.8 - - - +
345L HIS* 6.2 0.2 - - + -
351L ILE* 1.3 76.3 - - - +
353L VAL* 1.3 69.2 + - - +
372L ILE* 4.1 5.6 - - + -
373L ASP 3.6 4.3 - - - +
374L VAL* 3.7 21.3 - - + -
386L LEU* 6.0 0.2 - - + -
398L ASN* 3.9 38.8 - - + +
400L PHE* 3.7 40.4 - - + +
407L LEU* 4.9 2.0 - - + -
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Residues in contact with VAL 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L THR* 6.0 0.2 - - - +
312L ILE* 3.9 12.3 - - + -
329L HIS* 3.7 21.5 - - + +
331L HIS* 4.7 2.7 - - + -
340L ILE* 4.3 14.8 - - + -
341L LYS 5.2 1.6 - - - -
342L ALA* 3.3 32.8 - - + +
351L ILE* 3.7 14.8 - - + -
352L VAL* 1.3 82.3 - - - +
354L GLY* 1.3 81.4 + - - +
372L ILE* 3.7 7.5 - - - +
373L ASP* 2.9 35.2 + - + +
375L PHE* 5.7 5.4 - - + -
398L ASN* 5.2 5.2 - - - -
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Residues in contact with GLY 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329L HIS* 3.3 11.0 + - - -
331L HIS* 4.0 12.0 - - - +
340L ILE* 4.3 7.4 - - - +
341L LYS 5.8 0.6 + - - -
353L VAL* 1.3 83.6 - - - +
355L ARG* 1.3 61.6 + - - -
371L THR 4.2 4.0 - - - -
372L ILE* 4.4 9.0 - - - -
394L ILE* 6.1 0.2 - - - -
395L SER 3.9 21.5 - - - -
396L SER 5.1 5.5 + - - -
398L ASN* 5.3 4.2 - - - +
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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
------------------------------------------------------------
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