Contacts of the helix formed by residues 375 - 388 (chain M) in PDB entry 5D4E
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 SER 375 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114M PHE 3.6 18.6 + - - -
115M LEU* 3.6 21.7 - - - -
351M LEU* 4.1 9.0 - - - -
373M VAL* 4.1 2.8 + - - +
374M ASN* 1.3 73.9 + - - +
376M ARG* 1.3 67.3 + - - +
377M PRO* 3.4 1.1 - - - -
378M LEU* 3.3 5.1 + - - +
379M GLU* 2.8 43.7 + - - +
276P ARG* 5.3 1.3 - - - +
279P GLN* 3.1 20.6 + - - -
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Residues in contact with ARG 376 (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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374M ASN* 3.2 11.1 + - - +
375M SER* 1.3 79.9 - - - +
377M PRO* 1.3 60.7 - - + +
379M GLU* 2.6 43.1 + - - +
380M ALA* 2.9 31.1 + - - +
383M ARG* 4.9 3.5 + - - +
275P ALA* 4.9 3.6 + - - +
276P ARG* 3.6 40.0 - - - +
279P GLN* 3.6 21.4 - - - +
285P GLU* 3.3 32.9 + - - -
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Residues in contact with PRO 377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M GLY* 3.9 6.6 - - - +
350M ARG* 3.7 36.5 + - + +
351M LEU* 4.0 11.0 - - - +
354M GLY* 6.3 1.6 - - - -
358M ARG* 6.2 0.4 - - - +
374M ASN* 3.4 23.6 - - + +
375M SER 3.7 0.7 - - - -
376M ARG* 1.3 94.3 - - + +
378M LEU* 1.3 56.4 + - - +
380M ALA* 3.3 7.0 + - + +
381M ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 378 (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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94M LEU* 4.6 1.1 - - + -
115M LEU* 3.8 47.1 - - + +
344M PHE* 3.5 58.3 - - + +
347M GLY* 3.8 12.9 + - - +
348M LEU* 3.8 16.2 - - + +
351M LEU* 4.4 9.8 - - + +
375M SER 3.3 8.8 + - - +
377M PRO* 1.3 77.0 - - - +
379M GLU* 1.3 66.5 + - - +
381M ALA* 3.0 4.2 + - - +
382M ILE* 2.9 37.5 + - + +
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Residues in contact with GLU 379 (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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114M PHE* 5.6 0.2 - - - -
115M LEU 3.6 14.4 - - - +
116M GLY* 3.9 18.1 - - - -
117M HIS* 4.7 8.0 + - - +
375M SER* 2.8 30.1 + - - +
376M ARG* 2.6 36.9 + - - +
378M LEU* 1.3 76.2 - - - +
380M ALA* 1.3 56.7 + - - +
382M ILE* 4.0 7.2 - - - +
383M ARG* 2.9 51.5 + - - +
279P GLN* 3.9 3.0 + - - +
285P GLU* 3.7 9.7 - - - +
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Residues in contact with ALA 380 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M ARG* 5.2 6.3 - - - +
376M ARG 2.9 20.3 + - - +
377M PRO* 3.4 9.2 - - + +
379M GLU* 1.3 77.6 - - - +
381M ALA* 1.3 57.4 + - - +
383M ARG* 3.8 17.2 - - - +
384M GLU* 2.9 32.1 + - - +
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Residues in contact with ALA 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M GLN* 3.6 36.9 + - - +
346M VAL* 5.0 0.7 - - + -
347M GLY* 3.6 15.3 - - - +
350M ARG* 4.4 14.6 - - - +
377M PRO 2.9 16.3 + - - +
378M LEU 3.0 2.9 + - - +
380M ALA* 1.3 76.8 - - - +
382M ILE* 1.3 57.3 + - + +
384M GLU* 3.4 6.2 + - - +
385M PHE* 2.9 29.1 + - - +
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Residues in contact with ILE 382 (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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115M LEU 6.0 0.7 - - - +
117M HIS 4.3 9.2 - - - +
118M ILE* 3.7 26.5 - - + -
119M PRO* 3.7 30.1 - - + -
340M MET* 5.3 5.2 - - + +
343M GLN* 5.2 1.8 - - + -
344M PHE* 3.7 31.4 - - + +
378M LEU* 2.9 29.8 + - + +
379M GLU* 4.0 5.4 - - - +
381M ALA* 1.3 73.3 - - - +
383M ARG* 1.3 61.3 + - - +
385M PHE* 3.2 6.4 + - + +
386M PHE* 2.9 43.1 + - + -
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Residues in contact with ARG 383 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASN* 6.2 0.7 - - - +
376M ARG* 4.9 3.0 + - - +
379M GLU* 2.9 36.3 + - - +
380M ALA* 3.8 26.6 + - - +
382M ILE* 1.3 76.7 - - - +
384M GLU* 1.3 57.3 + - - +
386M PHE* 4.6 3.4 - - - +
387M SER* 2.9 48.5 + - - +
388M ARG* 4.6 15.0 - - - +
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Residues in contact with GLU 384 (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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343M GLN* 5.1 7.0 - - - +
350M ARG* 6.3 0.2 - - - +
380M ALA 2.9 21.4 + - - +
381M ALA* 3.4 7.9 - - - +
382M ILE 3.2 0.2 - - - -
383M ARG* 1.3 77.6 - - - +
385M PHE* 1.3 61.9 + - - +
388M ARG* 2.8 77.1 + - - +
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Residues in contact with PHE 385 (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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136M ILE* 3.8 32.5 - - + -
336M VAL* 4.7 1.1 - - + -
339M LEU* 3.5 37.9 - - + -
340M MET* 3.9 17.7 - - + -
343M GLN* 3.6 37.6 - - + +
381M ALA 2.9 9.9 + - - +
382M ILE* 3.2 7.2 + - - +
384M GLU* 1.3 76.7 - - - +
386M PHE* 1.3 91.7 + + - +
388M ARG 4.7 0.2 - - - -
389M SER* 3.2 39.5 - - - -
391M LEU* 5.5 4.9 - - + -
392M SER* 3.7 5.2 - - - -
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Residues in contact with PHE 386 (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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26M TYR* 3.7 20.9 - + - -
119M PRO* 3.5 24.9 - - + -
127M PHE* 3.5 36.1 - + - -
129M ILE* 3.9 32.3 - - + +
134M ARG* 3.6 12.4 - - + -
136M ILE* 4.2 12.8 - - + -
336M VAL* 5.4 0.4 - - + -
340M MET* 3.6 21.8 - - + -
382M ILE* 2.9 33.1 + - + +
383M ARG* 4.4 3.6 - - - +
385M PHE* 1.3 101.4 - + - +
387M SER* 1.3 60.7 + - - +
392M SER* 2.8 22.6 + - - -
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Residues in contact with SER 387 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M ILE* 3.9 19.0 - - - +
130M ASN* 4.0 12.0 + - - -
134M ARG* 3.6 25.3 + - - +
383M ARG* 2.9 29.2 + - - +
386M PHE* 1.3 81.8 - - - +
388M ARG* 1.3 89.9 + - - +
389M SER 3.8 2.5 + - - -
392M SER* 4.5 0.2 + - - -
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Residues in contact with ARG 388 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASN* 6.0 0.6 - - - +
383M ARG* 4.6 15.3 + - - +
384M GLU* 2.8 65.4 + - - +
385M PHE* 4.7 0.3 - - - -
387M SER* 1.3 104.3 + - - +
389M SER* 1.3 60.4 + - - +
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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