Contacts of the helix formed by residues 315 - 328 (chain E) in PDB entry 6C3P
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 ALA 315 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311E LEU 3.7 2.8 + - - +
312E LEU* 2.6 28.5 + - + +
314E PHE* 1.3 72.0 - - - +
316E GLY* 1.3 63.4 + - - +
317E PRO 3.6 0.4 - - - -
318E LEU* 3.7 24.9 - - + +
319E CYS* 3.6 14.4 + - - +
362E LEU* 4.4 3.1 - - - +
365E ALA* 6.1 4.0 - - + -
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Residues in contact with GLY 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY 2.9 15.7 + - - -
314E PHE 3.0 0.8 - - - -
315E ALA* 1.3 75.3 - - - +
317E PRO* 1.3 64.3 - - - +
319E CYS* 2.8 28.4 + - - +
320E ILE* 3.3 11.5 + - - +
362E LEU* 3.6 20.6 - - - +
366E LEU* 6.0 1.6 - - - -
585E ILE* 4.9 0.7 - - - -
1288E LEU* 4.7 8.3 - - - -
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Residues in contact with PRO 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY 4.2 0.2 - - - +
314E PHE* 3.3 18.8 - - + +
316E GLY* 1.3 88.7 - - - +
318E LEU* 1.3 61.2 + - + +
320E ILE* 2.8 26.7 + - + +
321E PHE* 2.9 14.8 + - - +
451E LEU* 5.8 2.2 - - + -
578E ALA* 4.2 14.1 - - + +
581E SER 4.7 0.2 - - - -
582E LEU* 3.8 40.2 - - + +
585E ILE* 3.6 29.2 - - + -
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E PHE* 4.8 4.9 - - + +
315E ALA* 3.7 29.8 - - + +
316E GLY 3.2 0.2 - - - -
317E PRO* 1.3 77.9 - - + +
319E CYS* 1.3 63.3 + - - +
321E PHE* 3.4 8.0 + - + +
322E GLY* 2.9 20.4 + - - -
451E LEU* 4.1 30.3 - - + -
454E TYR* 6.5 0.4 - - + -
455E ILE* 3.9 28.7 - - + -
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Residues in contact with CYS 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E ALA 3.6 5.1 + - - +
316E GLY 2.8 11.8 + - - +
318E LEU* 1.3 77.0 - - - +
320E ILE* 1.3 58.2 + - - +
323E ILE* 2.8 49.5 + - - +
358E LEU* 3.2 35.8 - - + +
359E ALA* 4.0 0.9 - - - -
362E LEU* 3.3 42.8 - - + +
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Residues in contact with ILE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E GLY 3.7 6.3 - - - +
317E PRO* 2.8 20.4 + - + +
319E CYS* 1.3 76.9 - - - +
321E PHE* 1.3 64.5 + - - +
323E ILE* 3.2 9.4 + - + +
324E VAL* 3.0 37.5 + - + +
362E LEU* 5.0 3.1 - - + -
577E PHE* 4.6 9.2 - - + -
578E ALA* 4.7 7.9 - - + +
581E SER* 3.6 23.1 - - - +
585E ILE* 5.3 0.2 - - + -
1281E GLY 4.7 0.2 - - - +
1284E LEU* 3.5 27.1 - - + -
1285E THR* 3.3 23.6 - - - +
1288E LEU* 3.8 27.4 - - + -
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Residues in contact with PHE 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E PRO 2.9 10.8 + - - +
318E LEU* 3.7 11.7 - - + +
320E ILE* 1.3 77.0 - - - +
322E GLY* 1.3 63.5 + - - +
324E VAL* 3.2 4.7 + - - +
325E ASP* 2.9 51.4 + - + +
455E ILE* 4.8 20.9 - - + -
456E LEU* 4.4 12.6 - - + -
574E SER* 3.1 28.7 - - - -
575E VAL* 4.1 18.2 - - + -
578E ALA* 4.1 21.0 - - + +
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Residues in contact with GLY 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E LEU 2.9 15.3 + - - -
319E CYS 3.7 2.7 - - - -
321E PHE* 1.3 75.9 - - - +
323E ILE* 1.3 64.7 + - - +
325E ASP* 2.6 16.1 - - - +
326E HIS* 2.3 41.4 + - - -
358E LEU* 4.1 9.0 - - - -
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Residues in contact with ILE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E CYS* 2.8 40.3 + - - +
320E ILE* 3.3 10.1 - - + +
322E GLY* 1.3 72.2 - - - +
324E VAL* 1.3 68.7 + - + +
326E HIS* 3.8 1.6 - - - +
327E LEU* 3.0 23.5 + - + +
355E ALA* 4.7 17.7 - - + +
358E LEU* 3.6 13.4 - - + +
359E ALA* 4.4 12.6 - - + -
362E LEU* 5.2 3.1 - - + -
1263E ALA* 5.2 4.9 - - + -
1267E ILE* 3.5 28.9 - - + +
1280E VAL* 4.6 3.1 - - + -
1284E LEU* 3.5 35.0 - - + -
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E ILE* 3.0 23.6 + - + +
321E PHE* 3.9 0.4 - - - +
323E ILE* 1.3 80.0 - - + +
325E ASP* 1.3 59.5 + - - +
327E LEU* 3.2 8.6 + - - +
328E GLY* 2.9 23.0 + - - -
573E PRO 4.7 2.7 - - - -
574E SER* 3.5 37.2 - - - +
577E PHE* 5.8 2.9 - - + -
578E ALA* 6.2 0.2 - - + -
1277E ALA* 4.7 21.3 - - + +
1278E GLY* 5.2 3.6 - - - +
1280E VAL* 6.3 0.2 - - + -
1281E GLY* 4.3 25.1 - - - +
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Residues in contact with ASP 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E PHE* 2.9 44.1 + - + +
322E GLY* 2.6 17.0 - - - +
324E VAL* 1.3 75.5 - - - +
326E HIS* 1.3 95.7 + - - +
328E GLY* 3.1 14.9 + - - +
329E LYS* 4.2 2.6 + - - +
574E SER* 4.4 11.7 - - - +
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Residues in contact with HIS 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E GLY* 2.3 35.8 + - - +
323E ILE 3.9 2.7 - - - +
325E ASP* 1.3 93.8 + - - +
327E LEU* 1.3 60.5 + - - +
329E LYS 4.0 11.3 + - - -
354E ASN* 2.9 45.1 + - - +
355E ALA* 4.3 12.1 - - + -
358E LEU* 3.8 23.1 - - + +
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Residues in contact with LEU 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ILE* 3.0 14.4 + - + +
324E VAL* 3.4 10.8 - - - +
325E ASP 3.2 0.2 - - - -
326E HIS* 1.3 73.4 - - - +
328E GLY* 1.3 67.2 + - - +
329E LYS* 2.8 12.2 + - - -
355E ALA* 5.4 2.2 - - + +
1267E ILE* 4.0 27.8 - - + +
1270E SER* 3.4 32.5 - - - +
1271E LEU* 4.4 25.8 - - + +
1277E ALA* 3.5 27.4 - - + -
1280E VAL* 4.6 4.3 - - + -
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Residues in contact with GLY 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E VAL 2.9 14.4 + - - -
325E ASP* 3.1 11.4 + - - -
327E LEU* 1.3 75.9 - - - +
329E LYS* 1.3 75.0 + - - +
1277E ALA* 6.4 0.2 - - - -
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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