Contacts of the strand formed by residues 327 - 331 (chain M) in PDB entry 5LN3
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 LYS 327 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M ILE* 4.0 31.6 - - + +
205M PRO* 4.5 15.7 - - - +
206M MET* 3.7 41.3 - - + +
219M PRO* 5.7 2.6 - - - +
220M PRO* 5.4 11.7 - - + +
221M LYS* 4.0 15.3 - - - +
280M PRO* 6.4 1.6 - - + -
281M SER 2.9 18.3 + - - +
282M ILE* 4.2 13.0 - - + -
283M ILE 2.9 23.1 + - - -
324M THR* 4.1 22.6 + - - +
326M VAL* 1.4 89.6 + - - +
328M VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202M ILE* 4.9 2.2 - - - +
221M LYS* 3.3 23.2 + - + +
222M GLY* 3.5 7.8 - - - -
223M VAL* 3.4 20.6 + - - +
282M ILE* 5.4 0.2 - - - -
283M ILE* 3.4 14.6 - - + +
285M ILE* 3.4 32.1 - - + -
313M LEU* 6.2 2.0 - - + -
317M LEU* 5.1 16.6 - - + -
326M VAL* 3.8 19.3 - - + -
327M LYS* 1.3 75.5 - - - +
329M ILE* 1.4 68.0 + - - +
330M ALA* 4.8 0.4 - - + +
348M LEU* 5.2 8.7 - - + -
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Residues in contact with ILE 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M LEU* 4.9 16.6 - - + -
202M ILE* 4.9 12.1 - - + -
223M VAL* 3.8 21.5 - - + -
225M MET* 5.5 8.1 - - + -
237M ALA* 4.2 24.7 - - + -
248M PHE* 5.6 0.4 - - + -
282M ILE* 3.9 24.0 - - + -
283M ILE 3.0 6.1 + - - +
284M PHE* 3.6 21.6 - - + -
285M ILE* 3.0 27.0 + - - +
328M VAL* 1.4 76.1 - - - +
330M ALA* 1.3 71.4 + - - +
331M ALA* 5.9 0.9 - - + -
352M ILE* 5.9 0.9 - - + -
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Residues in contact with ALA 330 (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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223M VAL 2.9 17.6 + - - +
224M LEU* 3.5 5.9 - - + -
225M MET* 3.1 21.9 + - - +
284M PHE* 4.9 0.4 - - - -
285M ILE* 3.7 19.3 - - + +
287M GLU 5.3 3.8 - - - +
288M LEU* 5.4 7.2 - - + -
328M VAL* 5.3 0.4 - - + -
329M ILE* 1.3 80.8 - - - +
331M ALA* 1.4 60.3 + - - +
348M LEU* 4.0 22.9 - - + -
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Residues in contact with ALA 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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224M LEU* 5.0 1.6 - - - -
225M MET* 3.6 16.8 - - + +
233M LYS* 5.9 7.9 - - + -
234M THR* 6.0 0.4 - - - +
284M PHE* 3.8 26.7 - - + -
285M ILE 3.3 6.4 + - - +
286M ASP* 5.1 0.4 - - - -
287M GLU 3.3 26.0 + - - +
288M LEU* 4.0 3.3 - - - +
329M ILE* 5.9 1.1 - - + -
330M ALA* 1.4 75.2 - - - +
332M THR* 1.4 70.3 + - - +
333M ASN* 4.9 2.7 - - - +
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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
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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