Contacts of the strand formed by residues 327 - 331 (chain I) in PDB entry 3V3K
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 ILE 327 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I PHE* 4.1 10.3 - - - +
262I VAL* 3.3 42.0 - - + +
265I PHE 5.1 1.6 - - - +
266I ASN* 5.2 5.2 - - + -
278I LYS* 3.7 32.8 - - + -
280I PHE* 4.4 3.4 - - + -
324I PRO* 3.4 27.8 - - + +
325I SER 4.0 0.4 - - - +
326I ASP* 1.3 78.8 - - - +
328I PHE* 1.3 66.9 + - - +
329I VAL* 4.0 15.5 - - + +
390I PHE 4.5 0.2 - - - -
393I PHE* 3.0 41.3 + - + +
394I LEU* 3.6 1.9 - - - +
334K PHE* 4.5 7.2 - - + -
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Residues in contact with PHE 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I LYS 3.2 5.8 + - - -
279I LEU* 3.5 23.3 - - + -
280I PHE* 2.7 33.1 + - - +
281I PHE* 5.3 2.2 - + - -
327I ILE* 1.3 78.6 - - - +
329I VAL* 1.3 56.8 + - - +
330I SER* 4.0 12.6 - - - -
366I LEU* 3.7 29.6 - - + -
367I GLN* 4.2 9.4 - - + -
370I LEU* 3.4 35.4 - - + -
389I CYS* 3.7 16.6 - - + -
390I PHE 3.8 3.1 - - - -
392I ASN* 3.5 34.8 - - + -
394I LEU* 3.4 26.5 - - + -
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Residues in contact with VAL 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I PHE* 4.1 10.5 - - + +
258I VAL* 3.9 1.8 - - + -
262I VAL* 3.4 30.7 - - + -
280I PHE* 3.5 10.8 - - + +
282I ILE* 3.7 24.2 - - + -
327I ILE* 4.0 12.8 - - + -
328I PHE* 1.3 74.3 - - - +
330I SER* 1.3 59.8 + - - +
331I TYR* 3.4 35.1 + - + +
389I CYS* 3.3 2.9 - - - -
390I PHE* 2.9 38.8 + - + -
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Residues in contact with SER 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280I PHE 2.8 13.0 + - - +
281I PHE* 3.8 8.2 - - - -
282I ILE* 3.1 28.6 + - - +
328I PHE* 3.8 9.4 + - - -
329I VAL* 1.3 71.5 - - - +
331I TYR* 1.3 58.8 + - - +
349I TYR* 2.6 29.9 + - - -
370I LEU* 3.2 31.4 - - - +
388I GLY 3.4 10.9 + - - -
389I CYS* 3.8 3.4 - - - -
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Residues in contact with TYR 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I PRO* 2.7 49.0 + - + +
241I GLY* 5.1 2.2 - - - -
258I VAL* 3.5 17.0 - - + +
282I ILE* 4.0 23.3 - - + -
329I VAL* 3.4 31.5 + - + +
330I SER* 1.3 77.3 + - - +
332I SER* 1.3 60.3 + - - +
333I THR 3.6 18.2 - - - +
335I PRO* 5.2 3.8 - - + -
349I TYR* 4.1 1.8 - - - -
387I PRO* 3.6 4.0 - - - +
388I GLY 3.0 35.3 + - - +
389I CYS* 5.0 0.9 - - - -
390I PHE* 4.5 5.6 - - + -
390K PHE* 3.7 38.4 - + - -
393K PHE* 5.1 3.4 - + + -
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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