Contacts of the helix formed by residues 347 - 361 (chain M) in PDB entry 5XTD
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 ASP 347 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346M VAL* 1.3 75.2 - - - +
348M ALA* 1.3 64.5 + - - +
349M GLU* 3.6 1.8 - - - +
350M ALA* 3.3 14.4 + - - +
351M LEU* 3.2 17.3 - - - +
592M LYS* 3.5 14.9 - - + +
594M ALA* 3.3 35.5 - - + +
595M THR 4.1 1.1 - - - +
596M TYR* 3.2 25.2 + - + +
618M GLU* 5.9 0.2 - - - +
619M ASP* 3.1 33.6 + - - +
620M TRP* 4.6 4.7 - - - -
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Residues in contact with ALA 348 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346M VAL 3.8 1.0 + - - -
347M ASP* 1.3 73.4 - - - +
349M GLU* 1.3 61.5 + - - +
351M LEU* 3.1 16.6 + - + +
352M VAL* 2.9 31.7 + - + +
524M ALA* 4.0 24.5 - - + -
528M LEU* 5.1 5.4 - - + -
530M TYR* 3.9 0.3 + - - -
595M THR* 3.8 11.1 + - + +
596M TYR* 4.9 1.4 - - - -
653M LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 349 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M ASP* 3.2 2.2 - - - +
348M ALA* 1.3 80.3 + - - +
350M ALA* 1.3 57.1 + - - +
352M VAL* 2.9 25.2 + - - +
353M ALA* 2.9 16.3 + - - +
594M ALA* 3.3 15.7 - - - +
595M THR* 2.8 50.1 + - - +
620M TRP* 3.9 22.1 - - + +
639M LEU* 4.1 17.6 - - + +
642M VAL* 4.2 16.1 - - + +
643M ARG* 4.1 9.4 + - - -
646M LEU* 4.6 13.7 - - + +
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Residues in contact with ALA 350 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346M VAL* 4.5 4.0 - - + -
347M ASP* 3.3 23.7 + - - +
348M ALA 3.3 0.4 - - - -
349M GLU* 1.3 79.3 - - - +
351M LEU* 1.3 58.8 + - + +
354M LEU* 2.9 33.0 + - - +
547M LEU* 5.0 5.8 - - + -
619M ASP* 3.4 24.2 - - - +
620M TRP* 3.6 15.4 - - + +
623M ILE* 3.2 15.4 - - + +
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Residues in contact with LEU 351 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M ALA* 4.5 16.4 - - + -
346M VAL* 3.5 32.8 - - + +
347M ASP 3.2 18.6 - - - +
348M ALA* 3.1 14.3 + - - +
350M ALA* 1.3 75.6 - - - +
352M VAL* 1.3 59.2 + - - +
354M LEU* 4.1 4.7 - - - +
355M LYS* 2.9 33.3 + - - +
368M THR* 5.7 0.7 - - + -
521M SER* 5.0 5.2 - - - +
524M ALA* 6.4 0.2 - - + -
525M ALA* 3.8 18.6 - - + +
530M TYR* 3.3 33.6 + - + +
547M LEU* 3.9 16.8 - - + -
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Residues in contact with VAL 352 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M ALA* 2.9 23.1 + - + +
349M GLU* 2.9 10.6 + - - +
351M LEU* 1.3 77.1 - - - +
353M ALA* 1.3 59.1 + - - +
355M LYS* 3.5 2.3 + - - +
356M ASP* 2.9 38.2 + - - +
528M LEU* 3.8 9.6 - - + -
530M TYR* 3.6 12.3 - - - +
636M TYR* 5.3 0.2 - - - +
642M VAL* 4.4 11.7 - - + -
645M ARG* 3.3 35.4 - - + +
646M LEU* 3.6 32.1 - - + -
649M VAL* 5.3 0.2 - - + -
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Residues in contact with ALA 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349M GLU 2.9 12.3 + - - +
350M ALA 4.1 2.5 - - - +
352M VAL* 1.3 77.1 - - - +
354M LEU* 1.3 58.3 + - - +
356M ASP* 3.3 8.3 + - - +
357M LEU* 2.9 25.8 + - - +
620M TRP* 4.3 10.3 - - + +
623M ILE* 3.6 24.8 - - + +
634M LEU* 3.7 12.5 - - + +
636M TYR* 3.2 25.4 - - - +
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Residues in contact with LEU 354 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330M LEU* 5.9 0.2 - - + -
340M ALA* 3.6 23.1 - - + -
350M ALA 2.9 19.8 + - - +
351M LEU* 4.1 2.9 - - - +
353M ALA* 1.3 76.0 - - - +
355M LYS* 1.3 60.1 + - - +
357M LEU* 3.1 28.8 + - + +
358M LEU* 2.9 35.8 + - + +
545M LEU* 3.5 36.3 - - + -
547M LEU* 3.6 27.4 - - + -
623M ILE* 3.8 15.2 - - + +
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Residues in contact with LYS 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU* 3.2 32.3 + - - -
20F ARG* 6.0 1.0 - - - +
68F ARG* 2.9 28.2 - - - +
74F GLU* 5.2 3.8 + - - -
351M LEU 2.9 19.4 + - - +
352M VAL* 3.9 2.9 - - - +
354M LEU* 1.3 78.3 - - - +
356M ASP* 1.3 60.7 + - - +
358M LEU* 3.0 8.5 + - + -
359M ASN* 2.8 39.4 + - - +
366M LEU* 3.6 30.1 - - + -
528M LEU 5.8 0.9 - - - -
530M TYR* 3.3 33.4 - - + -
645M ARG* 5.7 1.2 - - - +
649M VAL* 6.2 1.4 - - - +
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Residues in contact with ASP 356 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352M VAL* 2.9 30.0 + - - +
353M ALA* 3.4 9.7 - - - +
354M LEU 3.1 0.2 - - - -
355M LYS* 1.3 75.3 + - - +
357M LEU* 1.3 60.8 + - - +
359M ASN* 3.0 17.3 + - + +
360M ARG* 3.0 35.3 + - - +
634M LEU* 4.9 12.0 - - + +
636M TYR* 4.6 4.7 - - - -
645M ARG* 2.8 55.9 + - - -
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Residues in contact with LEU 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330M LEU* 3.8 31.6 - - + +
353M ALA 2.9 14.4 + - - +
354M LEU* 3.2 31.2 - - + +
356M ASP* 1.3 76.5 - - - +
358M LEU* 1.3 68.5 + - + +
359M ASN 3.1 0.7 + - - -
360M ARG* 3.4 12.5 + - - +
361M VAL* 3.2 22.4 + - + +
623M ILE* 4.8 9.6 - - + +
626M LEU* 4.4 12.3 - - + -
627M SER* 4.5 17.9 - - - -
630M ALA* 4.8 5.4 - - + -
632M MET* 3.5 28.5 - - + -
634M LEU* 5.3 1.1 - - - +
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Residues in contact with LEU 358 (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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330M LEU* 6.1 2.7 - - + -
338M VAL* 4.6 10.5 - - + -
339M ALA 5.4 2.2 - - - +
340M ALA* 4.3 20.2 - - + +
354M LEU* 2.9 23.6 + - + +
355M LYS* 3.0 9.6 + - + +
357M LEU* 1.3 86.8 - - + +
359M ASN* 1.3 61.3 - - - +
361M VAL* 3.6 6.7 - - + -
362M ASP* 2.9 4.7 + - - -
363M SER* 2.4 65.2 + - - +
365M THR* 3.2 29.6 - - - +
366M LEU* 4.1 11.2 - - + -
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Residues in contact with ASN 359 (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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68F ARG* 2.2 40.9 + - - +
71F PHE* 2.9 19.7 - - - -
72F GLY* 3.2 18.0 + - - +
74F GLU* 4.8 4.2 + - - -
355M LYS* 2.8 33.8 + - - +
356M ASP* 3.0 33.1 + - - +
358M LEU* 1.3 78.1 - - - +
360M ARG* 1.3 63.0 + - + +
362M ASP* 2.8 18.4 + - - +
645M ARG* 4.3 6.3 - - - +
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Residues in contact with ARG 360 (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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71F PHE* 3.2 37.0 - - - +
72F GLY* 5.9 0.2 - - - -
334M GLN* 5.2 0.5 - - - +
356M ASP* 3.0 21.7 + - - +
357M LEU* 3.4 2.9 + - - +
359M ASN* 1.3 76.9 - - - +
361M VAL* 1.3 59.6 + - - +
632M MET* 3.1 70.9 + - + +
633M THR 2.9 21.0 + - - -
634M LEU* 3.9 6.6 - - + +
635M PRO* 3.2 27.3 - - - +
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Residues in contact with VAL 361 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F PHE* 3.8 8.6 - - - -
330M LEU 4.5 11.4 - - - +
331M GLN* 6.0 0.7 - - - -
334M GLN* 3.4 33.5 - - + +
335M GLY* 2.9 24.1 + - - +
338M VAL* 5.7 0.2 - - + -
357M LEU* 3.2 18.6 - - + +
358M LEU* 3.6 13.5 - - + -
360M ARG* 1.3 77.1 - - - +
362M ASP* 1.3 65.2 + - - +
363M SER* 3.1 21.1 - - - +
632M MET* 3.7 31.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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