Contacts of the helix formed by residues 330 - 345 (chain P) in PDB entry 5A31
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 ARG 330 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C VAL* 4.6 16.6 - - - +
98C GLU* 2.7 36.3 + - - +
101C ARG* 5.6 0.4 - - - +
128C LYS* 5.7 2.2 - - - +
6M GLN* 5.1 14.9 - - - +
50P HIS* 5.5 4.9 - - - -
53P LYS* 5.5 6.5 - - - +
297P ILE* 2.9 30.0 - - + +
298P GLU* 5.8 3.4 - - - +
327P ASP* 3.0 37.3 + - + +
328P LYS 3.6 2.2 + - - -
329P TYR* 1.3 77.0 - - - +
331P VAL* 1.3 69.5 - - - +
332P GLU* 3.1 16.1 + - + +
333P THR* 2.9 20.2 - - + +
334P CYS* 3.2 8.5 + - - +
360P LEU* 3.8 9.9 - - - +
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Residues in contact with VAL 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLU* 5.2 1.3 - - - +
6M GLN* 3.4 28.5 - - - +
330P ARG* 1.3 75.0 - - - +
332P GLU* 1.3 75.3 + - - +
334P CYS 3.2 1.7 + - - -
335P CYS* 3.1 20.1 + - - +
357P ALA* 3.6 37.1 - - + +
360P LEU* 3.9 8.1 - - + -
361P ASN* 3.9 15.7 - - - +
364P TYR* 3.0 44.4 - - + -
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Residues in contact with GLU 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLU* 5.5 3.3 - - - +
297P ILE* 3.4 31.0 - - + +
298P GLU* 3.5 29.8 - - - +
300P MET* 5.0 1.3 - - + -
301P ASP* 4.2 18.8 - - + +
323P LEU* 4.8 0.4 - - - -
330P ARG* 3.1 17.2 + - + +
331P VAL* 1.3 95.6 + - - +
333P THR* 1.3 63.8 + - - +
335P CYS* 3.1 7.1 + - - -
336P VAL* 3.0 24.4 + - - +
364P TYR* 3.9 21.1 + - - +
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Residues in contact with THR 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P ILE* 4.4 4.8 - - - +
323P LEU* 3.8 34.0 - - - +
324P CYS* 3.9 9.9 + - - -
327P ASP 2.8 29.1 + - - +
328P LYS* 3.4 15.7 + - - +
330P ARG* 2.9 27.8 - - + +
332P GLU* 1.3 78.3 - - - +
334P CYS* 1.3 62.5 + - - +
336P VAL* 3.0 3.5 + - - +
337P ILE* 2.9 35.2 + - - +
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Residues in contact with CYS 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328P LYS 4.2 10.5 - - - -
330P ARG 3.2 12.4 + - - +
331P VAL 3.2 0.4 + - - -
333P THR* 1.3 77.5 - - - +
335P CYS* 1.3 57.5 + - - +
337P ILE* 3.6 5.6 + - - +
338P GLY* 3.1 20.4 + - - -
353P TYR* 3.6 31.7 - - - +
356P ARG* 3.3 47.6 - - - -
357P ALA* 3.6 23.6 - - + -
360P LEU* 5.1 5.2 - - + -
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Residues in contact with CYS 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301P ASP* 2.9 45.3 - - - +
331P VAL 3.1 12.6 + - - +
332P GLU 3.6 8.3 - - - +
334P CYS* 1.3 75.3 - - - +
336P VAL* 1.3 70.4 + - - +
338P GLY 3.1 0.5 + - - -
339P ASN* 2.8 28.4 + - - +
354P PHE* 3.4 25.6 - - + -
357P ALA* 4.0 6.8 - - + +
364P TYR* 5.1 4.0 - - + -
367P ALA* 5.0 5.8 - - + +
370P LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300P MET 3.8 15.0 - - - +
301P ASP* 4.4 1.3 - - - +
304P SER* 3.5 29.7 + - - +
316P LEU* 4.5 4.2 - - + +
319P LEU* 4.0 13.5 - - + -
320P ALA* 3.6 31.2 - - + -
323P LEU* 3.6 27.6 - - + -
332P GLU 3.0 11.8 + - - +
333P THR 3.0 8.4 + - - +
335P CYS* 1.3 77.0 - - - +
337P ILE* 1.3 59.6 + - + +
339P ASN* 3.0 5.9 + - - +
340P TYR* 2.9 25.8 + - - +
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Residues in contact with ILE 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O PHE* 3.3 42.4 - - + -
320P ALA* 4.1 13.9 - - + +
324P CYS* 4.0 14.8 - - + -
333P THR* 2.9 31.6 + - - +
334P CYS* 3.8 4.7 - - - +
336P VAL* 1.3 78.1 - - + +
338P GLY* 1.3 60.3 + - - +
340P TYR* 3.3 7.1 - - - +
341P TYR* 3.1 34.3 + - + -
353P TYR* 3.3 39.9 - - + -
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Residues in contact with GLY 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334P CYS 3.1 14.9 + - - -
335P CYS 3.1 3.7 + - - -
337P ILE* 1.3 72.5 - - - +
339P ASN* 1.3 66.2 + - - +
341P TYR* 3.2 2.0 + - - -
342P SER* 3.0 21.0 + - - -
350P ALA* 3.6 14.8 - - - +
353P TYR* 4.0 14.3 - - - +
354P PHE* 3.4 20.2 - - - -
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Residues in contact with ASN 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P SER* 2.7 32.7 + - - +
305P ASN* 3.2 30.3 + - - +
308P TYR* 3.8 28.3 - - + -
316P LEU* 4.5 3.8 - - + -
335P CYS* 2.8 19.4 + - - -
336P VAL 3.0 3.6 + - - +
338P GLY* 1.3 74.1 - - - +
340P TYR* 1.3 61.6 - - - +
342P SER* 2.7 24.2 + - - -
343P LEU* 3.0 14.0 + - - +
354P PHE* 3.4 5.2 - - - -
370P LEU* 4.2 15.1 - - - +
374P GLU* 5.5 0.5 - - - +
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Residues in contact with TYR 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O LEU* 3.9 6.3 - - + +
106O LYS* 3.9 14.1 + - + -
109O GLU* 3.1 44.5 + - - +
148O PHE* 3.4 32.1 - + - -
313P LYS* 5.6 3.6 - - + -
316P LEU* 3.3 31.8 - - + +
317P SER* 3.1 33.4 - - - -
320P ALA* 4.2 7.9 - - + -
336P VAL 2.9 9.7 + - - +
337P ILE* 3.3 16.4 - - - +
339P ASN* 1.3 77.2 - - - +
341P TYR* 1.3 65.5 + + - +
343P LEU* 3.5 3.8 + - - +
344P ARG* 3.2 36.3 + - + +
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Residues in contact with TYR 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O GLU* 3.4 34.3 + - - -
146O LEU 4.6 3.5 + - - -
148O PHE* 3.8 25.8 + + - +
151O VAL* 5.2 1.9 - - - +
337P ILE* 3.1 31.9 + - + -
338P GLY* 3.2 6.9 + - - +
340P TYR* 1.3 78.9 - + - +
342P SER* 1.3 61.4 + - - +
343P LEU 3.1 1.8 - - - -
344P ARG* 3.3 3.0 + - + +
345P SER 2.9 21.3 + - - -
346P GLN* 3.0 45.7 + - + +
349P LYS* 3.7 40.1 - - + +
350P ALA* 3.8 8.1 - - - +
353P TYR* 3.8 25.6 - + - -
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Residues in contact with SER 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308P TYR* 3.6 22.2 + - - -
338P GLY 3.0 12.7 + - - -
339P ASN* 2.7 27.7 + - - -
341P TYR* 1.3 75.3 - - - +
343P LEU* 1.3 56.8 + - - +
345P SER* 3.1 17.8 + - - -
347P HIS* 3.9 13.0 + - - -
350P ALA* 3.8 6.0 - - - +
354P PHE* 4.7 0.2 - - - -
374P GLU* 3.4 38.1 + - - -
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Residues in contact with LEU 343 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307P LEU 4.9 0.2 - - - +
308P TYR* 3.3 48.2 - - + +
311P SER* 4.5 25.4 - - - +
313P LYS* 3.7 37.0 + - + +
316P LEU* 4.3 18.8 - - + -
339P ASN 3.0 8.6 + - - +
340P TYR* 3.6 9.9 - - - +
341P TYR 3.1 0.2 - - - -
342P SER* 1.3 74.4 + - - +
344P ARG* 1.3 59.9 + - - +
345P SER* 3.0 8.1 + - - -
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Residues in contact with ARG 344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O LYS* 4.6 6.1 - - - -
109O GLU* 2.5 46.9 + - - +
110O GLN* 4.2 14.1 - - - +
113O ASP* 3.0 37.0 + - - +
143O TYR* 3.9 3.8 + - - -
313P LYS* 4.3 25.5 - - + +
340P TYR* 3.2 33.8 + - + +
341P TYR* 3.3 8.5 + - - +
343P LEU* 1.3 74.0 - - - +
345P SER* 1.3 68.0 + - - +
346P GLN* 2.6 32.8 + - - +
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Residues in contact with SER 345 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341P TYR 2.9 3.6 + - - -
342P SER 3.3 12.8 - - - -
343P LEU 3.0 6.1 - - - -
344P ARG* 1.3 82.0 - - - +
346P GLN* 1.3 61.9 + - - +
347P HIS* 3.4 26.4 + - - -
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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
------------------------------------------------------------
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