Contacts of the helix formed by residues 326 - 340 (chain P) in PDB entry 5C7O
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 PRO 326 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239P ARG* 6.2 0.2 - - - +
324P PRO* 3.4 12.8 - - + +
325P ALA* 1.3 90.9 - - - +
327P TYR* 1.3 60.7 + - - +
328P SER* 3.1 11.9 - - - +
329P ALA* 2.9 35.4 + - + +
330P ILE* 3.1 7.3 + - - +
377P ASP* 3.6 25.0 - - - +
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Residues in contact with TYR 327 (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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325P ALA 3.5 1.4 + - - -
326P PRO* 1.3 72.2 - - - +
328P SER* 1.3 57.4 + - - +
330P ILE* 3.1 18.6 + - + +
331P LYS* 3.0 58.7 + - + +
367P PHE* 3.6 19.1 - + - -
368P ASP 3.9 0.3 + - - -
369P ALA* 2.6 32.2 + - - -
372P GLY* 3.5 30.6 + - - -
373P ILE* 4.5 3.8 - - - -
374P ALA* 4.6 21.1 - - + -
380P VAL* 5.2 0.7 - - + -
381P LYS 4.7 0.4 - - - -
382P LEU* 4.0 20.7 - - + +
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Residues in contact with SER 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P PRO* 4.1 12.8 - - - +
327P TYR* 1.3 78.8 - - - +
329P ALA* 1.3 59.7 + - - +
331P LYS* 3.5 16.3 + - - +
332P GLU* 3.1 31.6 + - - +
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Residues in contact with ALA 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239P ARG* 4.1 15.1 + - - +
240P PHE* 3.6 20.5 - - + -
326P PRO* 2.9 26.0 + - + +
328P SER* 1.3 78.7 + - - +
330P ILE* 1.3 65.9 + - - +
332P GLU* 3.4 7.1 + - - +
333P ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 330 (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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236P ILE* 3.9 20.2 - - + -
240P PHE* 3.8 23.1 - - + -
321P LEU* 4.6 2.0 - - + -
325P ALA* 3.5 23.1 - - + +
326P PRO 3.1 7.8 + - - +
327P TYR* 3.1 24.6 + - + +
329P ALA* 1.3 78.2 - - - +
331P LYS* 1.3 61.4 + - - +
333P ALA* 3.3 2.9 + - - +
334P VAL* 3.1 23.7 + - + +
367P PHE* 4.1 14.1 - - + -
380P VAL* 4.1 30.7 - - + -
382P LEU* 4.1 17.5 - - + -
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Residues in contact with LYS 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P TYR* 3.0 44.9 + - + +
328P SER* 3.8 14.6 - - - +
330P ILE* 1.3 78.1 - - - +
332P GLU* 1.3 66.9 + - - +
334P VAL* 3.5 0.8 + - - -
335P LYS* 3.0 28.6 + - - +
348P TYR* 3.3 36.2 - - + +
350P GLU* 4.4 11.5 + - - +
367P PHE* 4.4 3.8 - - + -
369P ALA* 3.7 16.5 - - + +
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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
----------------------------------------------------------
328P SER 3.1 20.3 + - - +
329P ALA* 3.4 6.9 + - - +
330P ILE 3.3 0.2 - - - -
331P LYS* 1.3 77.6 - - - +
333P ALA* 1.3 57.8 + - - +
335P LYS* 3.2 35.1 + - - +
336P ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 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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235P VAL* 3.7 15.8 - - + +
236P ILE* 5.7 0.4 - - + -
239P ARG* 3.9 31.0 - - + +
240P PHE* 4.4 4.5 - - + -
329P ALA 3.1 18.1 + - - +
330P ILE 3.7 4.3 - - - +
332P GLU* 1.3 77.5 - - - +
334P VAL* 1.3 60.4 + - + +
336P ALA* 3.5 5.7 + - - +
337P ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 334 (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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232P LEU* 4.2 21.5 - - + -
235P VAL* 4.1 15.3 - - + -
236P ILE* 4.4 9.0 - - + -
330P ILE 3.1 17.7 + - - +
331P LYS 4.1 2.2 - - - +
333P ALA* 1.3 73.9 - - - +
335P LYS* 1.3 66.1 + - - +
337P ALA* 3.2 4.1 + - - +
338P ALA* 2.9 22.2 + - - +
346P LEU* 4.0 17.1 - - + +
348P TYR* 3.8 15.0 - - + -
367P PHE* 3.6 39.7 - - + -
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Residues in contact with LYS 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331P LYS* 3.0 15.7 + - - +
332P GLU* 3.2 34.9 + - - +
334P VAL* 1.3 76.9 - - - +
336P ALA* 1.3 62.5 + - - +
338P ALA* 3.2 2.9 + - - +
339P LYS* 3.1 52.8 + - + +
348P TYR* 3.7 45.0 + - + -
350P GLU* 3.9 12.7 + - - -
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Residues in contact with ALA 336 (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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332P GLU 3.0 18.5 + - - +
333P ALA* 3.8 6.1 - - - +
335P LYS* 1.3 76.1 - - - +
337P ALA* 1.3 64.3 + - - +
339P LYS* 3.3 9.1 + - - +
340P GLY* 3.1 17.2 + - - -
341P PRO* 3.8 5.6 - - - +
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Residues in contact with ALA 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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235P VAL* 3.5 33.2 - - + -
333P ALA 3.1 13.1 + - - +
334P VAL 3.2 7.8 + - - +
336P ALA* 1.3 77.4 - - - +
338P ALA* 1.3 60.5 + - - +
340P GLY 3.3 4.9 + - - -
341P PRO* 3.6 13.8 - - + -
342P MET* 2.9 34.8 + - + -
346P LEU* 4.1 5.8 - - + -
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Residues in contact with ALA 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P VAL 2.9 16.3 + - - +
335P LYS* 3.6 5.4 - - + +
337P ALA* 1.3 76.5 - - - +
339P LYS* 1.3 60.4 + - + +
342P MET 4.5 0.9 - - - -
343P ALA* 3.3 22.7 - - - +
344P GLY 4.6 0.5 + - - -
346P LEU* 3.1 32.8 - - + +
347P ALA* 4.0 14.6 - - - -
348P TYR* 4.2 8.7 - - + +
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Residues in contact with LYS 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335P LYS* 3.1 39.6 + - + +
336P ALA* 3.9 7.6 - - - +
337P ALA 3.2 0.2 - - - -
338P ALA* 1.3 79.0 - - + +
340P GLY* 1.3 58.8 + - - +
343P ALA* 4.3 6.8 - - - +
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Residues in contact with GLY 340 (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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336P ALA 3.1 8.2 + - - -
337P ALA 3.3 1.0 + - - -
339P LYS* 1.3 79.6 - - - +
341P PRO* 1.3 71.8 - - - +
342P MET 3.2 2.0 - - - -
343P ALA* 3.1 19.6 + - - +
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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
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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