Contacts of the strand formed by residues 309 - 315 (chain E) in PDB entry 1LT9
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 GLU 309 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245E GLU* 4.9 0.3 - - - +
249E TRP* 3.4 14.8 - - + -
308E THR* 1.3 77.1 - - - +
310E LEU* 1.3 60.7 + - - +
311E LEU 4.3 0.2 - - - -
325E HIS* 2.8 35.5 + - + -
326E TYR 3.3 12.1 - - - +
327E GLY* 3.8 9.9 - - - +
453E LYS 3.9 0.2 - - - +
454E ILE* 3.2 5.9 - - - -
455E ARG* 2.9 76.3 + - - +
456E PRO 3.4 12.1 - - - +
457E PHE* 3.9 21.9 - - + +
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Residues in contact with LEU 310 (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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249E TRP* 4.5 1.1 - - - -
252E ILE* 4.8 0.2 - - + -
308E THR 4.3 0.2 + - - -
309E GLU* 1.3 74.0 - - - +
311E LEU* 1.3 61.7 + - - +
312E ILE* 4.0 34.5 - - + -
324E ALA 3.8 0.5 - - - +
325E HIS* 3.4 5.6 - - - -
326E TYR* 2.8 50.4 + - + +
329E PHE* 3.7 46.2 - - + -
340E ILE* 5.8 0.2 - - + -
342E VAL* 4.3 6.3 - - + -
353E LEU* 4.5 3.4 - - + -
452E MET* 4.1 17.5 - - + -
453E LYS 3.3 26.0 - - - +
454E ILE* 4.3 7.6 - - + +
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Residues in contact with LEU 311 (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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244E THR* 4.0 14.6 - - + -
245E GLU* 4.4 4.5 - - - +
249E TRP* 3.6 43.7 - - + -
310E LEU* 1.3 73.5 - - - +
312E ILE* 1.3 64.3 + - - +
313E GLU* 3.5 30.9 + - + +
323E LYS* 4.0 31.9 - - + +
324E ALA 3.6 7.2 - - - +
325E HIS* 3.7 18.8 - - + -
451E SER 3.8 0.9 - - - +
452E MET* 3.6 1.6 - - - -
453E LYS* 2.7 39.6 + - + +
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Residues in contact with ILE 312 (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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310E LEU* 4.0 24.7 - - + -
311E LEU* 1.3 74.6 - - - +
313E GLU* 1.3 62.8 + - - +
314E MET* 4.0 7.3 - - + +
322E VAL 4.1 0.2 - - - +
323E LYS* 3.1 5.2 - - - +
324E ALA* 2.7 47.2 + - + +
326E TYR* 4.4 4.0 - - + -
353E LEU* 4.0 19.7 - - + -
402E TRP* 5.3 2.0 - - + -
412E PRO* 5.3 0.4 - - + -
437E TRP* 3.4 41.7 - - + -
450E MET* 3.9 17.0 - - - -
451E SER 3.3 10.3 - - - +
452E MET* 4.0 18.8 - - + -
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Residues in contact with GLU 313 (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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244E THR* 3.8 17.5 + - - +
311E LEU* 3.5 28.9 + - + +
312E ILE* 1.3 77.9 - - - +
314E MET* 1.3 62.6 + - - +
322E VAL 3.7 4.5 - - - +
323E LYS* 4.2 9.4 - - + -
450E MET* 3.2 4.7 - - - +
451E SER* 2.8 41.5 + - - +
453E LYS* 2.8 43.6 + - - +
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Residues in contact with MET 314 (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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312E ILE* 4.0 19.3 - - + +
313E GLU* 1.3 77.0 - - - +
315E GLU* 1.3 63.5 + - - +
321E LYS* 3.4 7.6 - - - +
322E VAL* 3.1 53.4 + - + +
349E ALA* 3.6 19.1 - - + -
437E TRP* 3.6 42.0 - - + -
440E TRP* 3.9 7.2 - - + -
447E MET* 3.4 29.8 - - + -
449E LYS* 3.4 15.7 - - - +
450E MET* 4.1 8.1 - - + -
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Residues in contact with GLU 315 (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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314E MET* 1.3 79.8 - - - +
316E ASP* 1.3 66.4 + - - +
319E GLY* 4.1 11.7 - - - +
320E ASP 3.1 15.9 - - - +
321E LYS* 2.6 37.7 + - - +
440E TRP* 4.3 1.3 - - - -
447E MET* 3.5 6.4 - - - +
448E ARG* 3.0 58.0 + - - -
449E LYS* 3.1 35.3 + - + +
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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