Contacts of the helix formed by residues 312 - 327 (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 MET 312 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283P LEU* 3.1 37.5 - - + -
307P LEU* 3.5 31.0 + - + +
310P ARG* 3.4 34.8 - - + +
311P SER* 1.3 70.2 - - - +
313P LYS* 1.3 63.1 + - - +
314P SER* 3.2 3.4 - - - -
315P GLU* 3.2 38.0 + - + +
316P LEU* 3.0 22.3 + - - +
343P LEU* 4.9 1.1 - - - +
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Residues in contact with LYS 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O LYS* 4.2 32.8 - - + -
110O GLN* 5.3 7.7 + - - -
311P SER 2.9 10.6 + - - +
312P MET* 1.3 68.6 - - - +
314P SER* 1.3 67.1 + - - +
316P LEU* 3.3 6.5 + - + +
317P SER* 2.9 31.6 + - - +
340P TYR* 5.1 3.3 - - + +
343P LEU* 3.7 52.9 + - + +
344P ARG* 4.2 23.1 - - + +
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Residues in contact with SER 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 2.7 46.2 + - - +
106O LYS* 4.4 17.9 - - - +
312P MET* 3.2 1.7 - - - -
313P LYS* 1.3 79.5 - - - +
315P GLU* 1.3 66.8 + - - +
317P SER* 3.3 0.6 + - - -
318P TYR 3.1 11.6 + - - -
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Residues in contact with GLU 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 5.0 0.2 - - - -
283P LEU* 4.9 4.0 - - - +
287P ASN* 5.8 2.5 + - - -
307P LEU* 3.2 29.2 - - + +
312P MET* 3.2 38.0 + - + +
314P SER* 1.3 82.8 - - - +
316P LEU* 1.3 61.5 + - - +
318P TYR* 3.3 9.7 + - - +
319P LEU* 3.1 21.8 + - - +
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Residues in contact with LEU 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304P SER* 3.8 33.0 - - - +
307P LEU* 3.4 24.4 - - + +
308P TYR* 4.7 2.7 - - - +
312P MET 3.0 15.8 + - - +
313P LYS* 3.3 9.6 + - + +
315P GLU* 1.3 77.8 - - - +
317P SER* 1.3 55.7 + - - +
319P LEU* 3.2 7.9 + - + +
320P ALA* 2.9 26.3 + - + +
336P VAL* 4.5 3.6 - - + +
339P ASN* 4.8 2.9 - - + -
340P TYR* 3.3 48.7 - - + +
343P LEU* 4.3 15.7 - - + -
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Residues in contact with SER 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 4.0 20.6 - - - -
105O LEU* 4.6 4.8 - - - +
106O LYS* 3.4 19.7 - - - +
148O PHE* 5.5 0.3 - - - -
313P LYS* 2.9 18.3 + - - +
314P SER 3.8 3.8 - - - -
316P LEU* 1.3 73.0 - - - +
318P TYR* 1.3 67.9 + - - +
320P ALA* 4.2 1.2 - - - +
321P HIS* 3.3 26.0 + - - +
340P TYR* 3.1 31.6 - - - -
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Residues in contact with TYR 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 3.6 25.3 - - + +
290P ARG* 4.7 9.4 - - - -
314P SER 3.1 7.2 + - - +
315P GLU* 3.4 13.2 - - - +
316P LEU 3.2 0.2 - - - -
317P SER* 1.3 76.7 - - - +
319P LEU* 1.3 65.0 + - - +
321P HIS* 3.7 23.2 + + - -
322P ASN* 3.1 49.0 + - - +
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Residues in contact with LEU 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290P ARG* 3.0 37.0 - - - +
300P MET* 4.0 12.3 - - + +
303P PHE* 3.9 37.9 - - + -
304P SER* 4.1 21.8 - - - +
307P LEU* 4.2 7.4 - - + -
315P GLU 3.1 9.2 + - - +
316P LEU* 3.5 9.4 - - + +
318P TYR* 1.3 81.4 - - - +
320P ALA* 1.3 63.0 + - - +
322P ASN* 3.1 2.8 + - - +
323P LEU* 3.0 37.4 + - + +
336P VAL* 4.0 11.2 - - + -
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Residues in contact with ALA 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148O PHE* 3.9 19.6 - - + -
316P LEU 2.9 20.0 + - - +
317P SER 4.2 2.5 - - - +
319P LEU* 1.3 73.4 - - - +
321P HIS* 1.3 62.8 + - - +
323P LEU* 3.5 2.0 + - - +
324P CYS* 3.2 23.4 + - - +
336P VAL* 3.6 23.1 - - + -
337P ILE* 4.1 12.0 - - + +
340P TYR* 4.2 19.3 - - + -
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Residues in contact with HIS 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 5.4 4.7 - - + +
105O LEU* 4.2 17.8 + - + +
148O PHE* 4.0 8.9 - - - -
152O PHE* 3.2 53.5 - + + -
155O TYR* 5.2 8.8 - + - -
317P SER 3.3 19.5 + - - +
318P TYR* 3.7 30.2 + + - -
320P ALA* 1.3 79.0 - - - +
322P ASN* 1.3 76.2 + - - +
324P CYS* 3.6 2.6 + - - +
325P GLU* 3.2 22.3 + - - +
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Residues in contact with ASN 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290P ARG* 3.8 22.8 - - - +
294P PRO 5.6 1.1 - - - +
318P TYR* 3.1 48.4 + - - +
319P LEU 3.1 5.8 + - - +
321P HIS* 1.3 86.6 + - + +
323P LEU* 1.3 61.3 + - - +
325P GLU* 3.3 8.7 + - - +
326P ILE* 3.2 32.4 + - - +
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Residues in contact with LEU 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290P ARG* 3.8 16.4 - - - +
296P ARG 4.6 4.0 - - - +
297P ILE* 3.7 23.6 - - + +
300P MET* 4.0 15.7 - - + -
319P LEU* 3.0 25.0 + - + +
320P ALA* 3.9 4.0 - - - +
321P HIS 3.4 0.2 - - - -
322P ASN* 1.3 74.7 - - - +
324P CYS* 1.3 64.5 + - - +
326P ILE* 2.9 14.0 + - + +
327P ASP 2.9 27.5 + - - +
333P THR* 3.8 26.7 - - - +
336P VAL* 3.6 39.3 - - + -
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Residues in contact with CYS 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148O PHE* 3.7 20.9 - - + -
149O SER* 3.5 41.9 + - - -
152O PHE* 5.3 6.5 - - + -
153O LYS* 5.9 0.7 + - - -
320P ALA 3.2 15.3 + - - +
321P HIS* 3.7 4.9 - - - +
323P LEU* 1.3 79.4 - - - +
325P GLU* 1.3 62.0 + - - +
328P LYS* 3.7 32.3 + - - +
333P THR* 3.9 8.4 + - - -
337P ILE* 4.0 8.5 - - + -
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Residues in contact with GLU 325 (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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100C ASP* 5.3 0.7 - - - +
129C LYS* 3.9 30.3 + - + +
152O PHE* 3.2 29.6 - - + -
153O LYS* 3.5 24.4 + - - +
321P HIS* 3.2 10.4 + - - +
322P ASN* 3.4 15.7 - - - +
323P LEU 3.1 0.6 - - - -
324P CYS* 1.3 78.5 - - - +
326P ILE* 1.3 67.4 + - + +
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Residues in contact with ILE 326 (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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98C GLU* 6.1 0.9 - - + +
100C ASP* 4.5 22.5 - - + +
128C LYS* 5.3 2.4 - - - -
129C LYS* 5.1 6.2 - - - +
290P ARG* 5.3 2.9 - - - +
294P PRO 4.5 4.7 - - - +
295P TYR* 4.0 56.8 - - + +
296P ARG 5.0 0.9 - - - +
297P ILE* 4.5 5.8 - - + -
322P ASN* 3.2 32.3 + - - +
323P LEU* 2.9 22.1 + - + +
325P GLU* 1.3 81.4 - - + +
327P ASP* 1.3 83.8 + - + +
328P LYS 4.0 0.6 + - - -
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Residues in contact with ASP 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 4.0 13.8 - - - +
100C ASP* 5.0 5.0 - - - +
128C LYS* 3.2 30.2 + - - +
132C ASP* 5.9 0.2 - - - -
297P ILE* 4.1 7.4 - - + +
323P LEU 2.9 12.0 + - - -
326P ILE* 1.3 94.1 - - + +
328P LYS* 1.3 60.5 + - - +
329P TYR 3.3 4.0 + - - +
330P ARG* 3.0 44.5 + - + +
333P THR* 2.8 27.0 - - - +
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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