Contacts of the strand formed by residues 327 - 333 (chain E) in PDB entry 5LS6
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 ALA 327 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E HIS* 5.0 1.0 - - - -
322E LYS* 3.9 10.6 - - - +
323E SER 4.4 3.6 + - - +
325E GLU* 3.6 7.7 - - + +
326E ASN* 1.3 79.4 + - - +
328E ILE* 1.3 67.0 + - - +
329E VAL* 3.8 12.6 + - + +
355E ARG* 4.4 15.3 - - + +
356E PHE 3.6 9.6 - - - +
357E ASP* 4.0 16.8 - - - +
358E TYR* 3.3 20.6 + - - -
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Residues in contact with ILE 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E LEU* 4.3 15.3 - - + -
321E SER 3.8 13.2 - - - +
322E LYS* 4.1 3.8 - - + -
327E ALA* 1.3 71.7 - - - +
329E VAL* 1.3 61.8 + - - +
355E ARG* 3.6 2.9 - - - -
356E PHE* 2.8 43.2 + - + +
358E TYR* 3.4 15.4 - - + -
368E PHE* 3.5 52.7 - - + -
377E LEU* 3.7 28.7 - - + -
379E LEU* 4.1 7.6 - - + -
389E TRP* 4.1 15.9 - - + -
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Residues in contact with VAL 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E ILE* 4.1 8.3 - - + +
305E HIS* 4.1 19.1 - - + +
319E ILE 3.4 0.5 - - - +
320E LEU* 4.4 2.7 - - - -
321E SER 2.9 35.8 + - - +
325E GLU* 5.4 3.1 - - - +
327E ALA* 4.2 10.8 - - + +
328E ILE* 1.3 77.0 - - - +
330E CYS* 1.3 62.9 + - - +
331E TRP* 3.3 10.6 - - + -
352E ILE* 3.5 44.4 - - + -
354E GLY 3.8 3.4 - - - +
355E ARG* 4.1 26.9 - - + +
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Residues in contact with CYS 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.8 28.7 - - + -
315E LEU* 4.2 6.3 - - - -
318E LEU* 3.9 26.9 - - - -
319E ILE 3.1 7.9 - - - -
320E LEU* 3.7 18.8 - - + +
328E ILE 4.1 1.2 + - - -
329E VAL* 1.3 70.5 - - - +
331E TRP* 1.3 61.4 + - - +
352E ILE* 3.8 3.3 - - - +
353E LEU* 2.9 25.4 + - - -
354E GLY* 2.9 22.5 + - - +
356E PHE* 4.3 10.3 - - + -
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Residues in contact with TRP 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E MET* 4.0 17.5 - - + -
260E LEU* 3.4 39.4 - - + +
299E PHE* 4.0 14.4 - + - -
301E THR* 3.8 21.3 - - + -
304E ILE* 3.5 25.8 - - + -
318E LEU* 3.8 5.5 - - - +
319E ILE* 3.0 56.5 + - + +
321E SER* 3.0 20.5 + - - -
329E VAL 3.3 17.7 - - - -
330E CYS* 1.3 73.0 - - - +
332E LYS* 1.3 88.8 + - - +
333E PRO* 4.1 2.2 - - + -
350E VAL* 4.0 2.7 - - + -
351E THR 3.4 9.9 - - - +
352E ILE* 3.5 24.9 - - + -
353E LEU* 4.2 4.0 - - - +
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Residues in contact with LYS 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D MET* 4.1 15.2 - - + +
317E ASP 4.8 5.6 - - - +
318E LEU* 4.2 20.6 - - + -
319E ILE* 4.6 1.1 - - - -
331E TRP* 1.3 86.7 - - - +
333E PRO* 1.4 80.4 - - + +
335E LYS 3.9 4.0 - - - +
336E MET* 2.7 43.1 + - + +
337E GLU 4.0 2.0 + - - -
338E ASP 2.7 31.5 + - - +
339E ASP* 4.8 1.8 - - - +
340E ILE* 5.3 4.4 - - - +
350E VAL* 3.2 7.4 - - - +
351E THR* 3.0 46.4 + - - +
353E LEU* 4.5 2.7 - - + -
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Residues in contact with PRO 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E MET* 4.6 7.6 - - + -
262E LEU* 5.1 1.3 - - + -
299E PHE* 3.6 40.4 - - + -
317E ASP 5.3 1.8 - - - +
319E ILE* 4.5 7.4 - - + -
331E TRP* 4.3 7.0 - - + -
332E LYS* 1.4 106.9 - - + +
334E GLY* 1.3 61.7 + - - +
338E ASP 4.0 4.9 - - - +
339E ASP 5.6 0.2 - - - -
340E ILE* 3.4 29.7 - - + +
343E ILE* 4.1 19.9 - - + +
349E ASN 3.8 5.8 - - - +
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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