Contacts of the helix formed by residues 373 - 388 (chain E) in PDB entry 6XAV
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 THR 373 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372E THR* 1.3 79.3 - - - +
374E GLN* 1.3 61.5 + - - +
375E GLU* 3.0 31.6 + - - +
376E GLU* 3.3 22.0 + - - +
377E LEU* 2.9 27.9 + - - +
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Residues in contact with GLN 374 (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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373E THR* 1.3 74.9 - - - +
375E GLU* 1.3 69.3 + - - +
377E LEU* 3.4 8.0 + - + +
378E GLN* 3.1 24.6 + - + +
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Residues in contact with GLU 375 (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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373E THR* 3.0 26.7 + - - +
374E GLN* 1.3 83.9 + - - +
376E GLU* 1.3 59.4 + - - +
378E GLN* 3.4 11.5 + - - +
379E LYS* 3.1 49.1 + - - +
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Residues in contact with GLU 376 (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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144E ARG* 3.7 14.8 + - - -
146E ARG* 4.4 16.7 + - - -
164E LEU* 5.4 2.3 - - - +
371E LEU 4.8 0.2 - - - +
372E THR* 3.5 26.1 - - - +
373E THR* 3.3 29.7 + - - +
375E GLU* 1.3 78.3 - - + +
377E LEU* 1.3 65.3 + - - +
379E LYS* 3.3 9.7 + - - +
380E MET* 3.1 49.6 + - + +
413E PHE* 5.3 8.9 - - + -
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Residues in contact with LEU 377 (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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368E GLU* 3.3 38.6 - - + +
369E GLU* 4.3 24.0 - - + +
372E THR* 4.1 12.0 + - - +
373E THR 2.9 17.9 + - - +
374E GLN* 3.7 7.2 - - - +
375E GLU 3.3 0.2 - - - -
376E GLU* 1.3 76.3 - - - +
378E GLN* 1.3 61.8 + - - +
380E MET* 3.4 10.1 + - + +
381E TRP* 3.1 21.6 + - + +
353F ARG* 5.0 8.3 - - - +
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Residues in contact with GLN 378 (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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374E GLN* 3.1 18.9 + - + +
375E GLU* 3.7 11.6 - - - +
376E GLU 3.2 0.2 - - - -
377E LEU* 1.3 75.0 - - - +
379E LYS* 1.3 60.5 + - + +
381E TRP* 3.1 13.8 + - + +
382E ILE* 3.0 51.9 + - + +
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Residues in contact with LYS 379 (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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375E GLU* 3.1 33.8 + - - +
376E GLU* 3.8 7.9 - - - +
378E GLN* 1.3 77.7 - - + +
380E MET* 1.3 58.9 + - - +
382E ILE* 3.5 10.8 + - + +
383E LEU* 3.0 27.7 + - - +
410E ASP* 4.8 8.9 + - - -
413E PHE* 3.6 53.3 - - + +
414E GLU* 4.7 6.1 + - - +
417E LYS* 3.7 42.4 - - + +
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Residues in contact with MET 380 (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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163E ASP 3.4 24.5 - - - +
164E LEU* 3.8 32.8 - - + +
165E ALA 5.6 0.7 - - - +
167E PRO* 4.3 6.3 - - + -
360E TYR* 4.3 2.8 + - - +
368E GLU* 4.8 11.7 - - - +
372E THR* 4.0 16.6 - - + -
376E GLU* 3.1 48.0 + - + +
377E LEU* 3.8 12.3 - - + +
379E LYS* 1.3 76.9 - - - +
381E TRP* 1.3 59.6 + - - +
383E LEU* 3.4 7.4 + - - +
384E ARG* 3.0 39.9 + - - +
413E PHE* 5.0 9.4 - - + -
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Residues in contact with TRP 381 (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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377E LEU* 3.1 15.1 + - + +
378E GLN* 3.1 16.6 + - + +
380E MET* 1.3 74.2 - - - +
382E ILE* 1.3 95.2 + - + +
384E ARG* 3.3 10.7 + - + +
385E LYS* 3.1 60.2 + - + +
352F LYS 5.0 7.0 + - - -
353F ARG* 3.8 37.8 - - - +
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Residues in contact with ILE 382 (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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378E GLN* 3.0 35.7 + - + +
379E LYS* 3.9 11.2 - - + +
380E MET 3.4 0.2 - - - -
381E TRP* 1.3 97.5 - - + +
383E LEU* 1.3 61.5 + - - +
385E LYS* 3.3 13.9 + - + +
386E ILE* 3.3 31.4 + - + +
416E MET* 6.6 0.2 - - + -
417E LYS* 5.8 8.5 - - + -
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Residues in contact with LEU 383 (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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164E LEU* 4.5 15.9 - - + -
360E TYR* 3.3 24.9 - - + +
379E LYS 3.0 18.3 + - - +
380E MET* 3.7 6.5 - - - +
381E TRP 3.2 0.2 - - - -
382E ILE* 1.3 78.3 - - - +
384E ARG* 1.3 56.9 + - - +
386E ILE* 3.3 8.1 + - + -
387E ILE* 3.0 55.4 + - + +
398E PHE* 4.6 12.6 - - + -
399E LEU* 5.2 9.2 - - + -
412E PHE* 4.4 22.2 - - + -
413E PHE* 4.4 20.0 - - + -
416E MET* 6.2 2.2 - - + -
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Residues in contact with ARG 384 (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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164E LEU 5.0 1.0 + - - -
165E ALA* 3.3 29.3 + - - +
360E TYR* 3.1 47.2 + - + -
361E ASN* 3.9 9.4 + - - +
363E SER 3.5 25.8 + - - -
364E GLY* 3.9 5.8 - - - -
368E GLU* 5.2 6.7 + - - -
380E MET* 3.0 27.4 + - - +
381E TRP* 3.7 8.5 - - + +
382E ILE 3.3 0.2 - - - -
383E LEU* 1.3 77.5 - - - +
385E LYS* 1.3 65.9 + - - +
387E ILE* 4.4 1.8 - - - +
388E HIS* 2.9 35.8 + - + +
353F ARG* 4.0 28.6 - - - +
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Residues in contact with LYS 385 (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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381E TRP* 3.1 63.4 + - + +
382E ILE* 3.3 8.2 + - + +
384E ARG* 1.3 83.8 - - - +
386E ILE* 1.3 60.0 + - + +
388E HIS* 5.0 10.2 + - + +
389E PRO* 3.1 22.6 - - - +
351F GLU 4.4 14.5 + - - -
352F LYS* 4.6 18.7 + - + +
353F ARG* 6.5 0.2 - - - +
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Residues in contact with ILE 386 (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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382E ILE* 3.3 31.5 + - + +
383E LEU* 3.3 8.7 + - + +
384E ARG 3.1 0.6 - - - -
385E LYS* 1.3 81.9 - - + +
387E ILE* 1.3 62.4 + - - +
388E HIS 3.4 0.2 - - - -
389E PRO* 3.3 10.0 - - - +
390E MET* 3.8 26.4 - - + +
398E PHE* 4.2 26.5 - - + -
416E MET* 4.6 21.1 - - + -
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Residues in contact with ILE 387 (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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360E TYR* 3.7 40.2 - - + -
361E ASN* 3.7 16.8 + - - +
383E LEU* 3.0 44.0 + - + +
384E ARG 4.2 1.3 - - - +
386E ILE* 1.3 78.1 - - + +
388E HIS* 1.3 65.4 + - - +
390E MET* 3.2 26.0 + - - +
395E ALA* 3.6 29.4 - - + +
396E MET* 6.1 0.9 - - + -
398E PHE* 4.5 17.7 - - + -
399E LEU* 5.1 12.6 - - + -
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Residues in contact with HIS 388 (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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361E ASN* 3.6 33.3 + - + +
384E ARG* 2.9 20.3 + - + +
385E LYS* 4.9 10.0 + - - +
387E ILE* 1.3 76.3 - - - +
389E PRO* 1.3 73.0 - - + +
390E MET 3.2 8.0 - - - +
351F GLU* 5.0 8.9 + - - -
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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