Contacts of the strand formed by residues 327 - 331 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M PHE* 3.8 16.6 - - - +
262M VAL* 3.4 41.1 - - + +
265M PHE 5.1 1.3 - - - +
266M ASN* 5.3 5.6 - - + -
278M LYS* 3.7 33.7 - - + -
280M PHE* 4.4 4.7 - - + -
324M PRO* 3.4 27.6 - - + +
325M SER 3.9 1.8 - - - +
326M ASP* 1.3 77.8 - - - +
328M PHE* 1.3 66.0 + - - +
329M VAL* 3.9 9.6 - - + -
390M PHE 4.6 0.9 - - - +
393M PHE* 2.9 38.5 + - + -
394M LEU 3.7 0.3 + - - -
334O PHE* 4.6 6.7 - - + -
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Residues in contact with PHE 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278M LYS 3.3 6.3 + - - -
279M LEU* 3.5 21.8 - - + -
280M PHE* 2.7 34.2 + - - +
281M PHE* 4.9 2.5 - + - -
327M ILE* 1.3 77.2 - - - +
329M VAL* 1.3 56.3 + - - +
330M SER* 4.2 11.7 - - - -
366M LEU* 3.6 28.7 - - + -
367M GLN* 4.2 9.2 - - + -
370M LEU* 3.4 34.5 - - + -
389M CYS* 3.7 23.1 - - + -
390M PHE 3.8 2.5 - - - -
392M ASN* 3.5 41.1 - - - -
394M LEU* 3.7 19.1 - - + -
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Residues in contact with VAL 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240M PHE* 4.0 11.4 - - - -
258M VAL* 3.9 3.4 - - + -
262M VAL* 3.6 28.0 - - + -
280M PHE* 3.4 8.7 - - + -
282M ILE* 3.5 30.1 - - + -
327M ILE* 3.9 13.5 - - + -
328M PHE* 1.3 76.1 - - - +
330M SER* 1.3 59.3 + - - +
331M TYR* 3.4 32.5 - - + +
389M CYS* 3.2 3.9 - - - -
390M PHE* 2.8 39.0 + - + +
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Residues in contact with SER 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280M PHE 2.7 9.3 + - - -
281M PHE* 3.7 16.6 - - - -
282M ILE 3.1 24.6 + - - -
328M PHE* 4.0 5.0 - - - -
329M VAL* 1.3 69.2 - - - +
331M TYR* 1.3 62.1 + - - +
332M SER 3.8 0.2 + - - -
349M TYR* 2.6 30.0 + - - -
370M LEU* 3.2 32.6 - - - +
388M GLY 3.4 11.0 + - - -
389M CYS* 3.9 2.4 - - - +
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Residues in contact with TYR 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M PRO* 2.7 66.1 + - + +
241M GLY* 4.7 3.8 - - - -
258M VAL* 3.8 14.5 - - + +
282M ILE* 4.1 13.5 - - + -
286M GLY* 6.5 0.7 - - - -
329M VAL* 3.4 36.2 - - + +
330M SER* 1.3 72.0 - - - +
332M SER* 1.3 60.7 + - - +
333M THR 3.5 19.7 - - - +
335M PRO* 5.0 8.5 - - + -
349M TYR* 4.1 2.9 - - - -
387M PRO* 3.6 3.8 - - - +
388M GLY 3.0 35.2 + - - +
389M CYS* 4.8 0.7 - - - -
390M PHE* 4.4 7.2 - - + -
390O PHE* 4.3 23.3 - + - -
393O PHE* 5.1 4.7 - - + -
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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