Contacts of the helix formed by residues 338 - 348 (chain C) in PDB entry 6CP3
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 338 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293C ARG* 5.1 0.2 - - - +
294C GLU* 5.1 11.4 - - - +
331C THR* 6.4 1.1 - - - -
332C GLN* 6.1 7.6 - - + +
335C ASP* 3.0 13.2 + - + +
336C VAL 3.2 2.5 - - - +
337C SER* 1.3 78.7 - - - +
339C TYR* 1.3 58.9 + - - +
340C ILE* 3.3 1.3 - - + +
341C PRO* 3.3 19.0 - - + +
342C THR* 2.6 35.6 + - - -
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Residues in contact with TYR 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ARG* 3.2 68.8 + - + +
294C GLU* 4.6 18.0 + - + +
296C TYR* 4.4 14.1 - + + -
297C PRO 4.7 3.0 + - - -
298C GLY* 4.5 12.5 + - - -
300C VAL* 3.6 26.6 - - + +
301C PHE* 5.2 2.1 + - - +
338C ALA* 1.3 74.9 - - - +
340C ILE* 1.3 62.5 + - + +
342C THR* 3.8 3.9 - - - -
343C ASN* 2.9 50.0 + - - -
263D GLN* 4.8 9.5 + - - +
266D SER* 6.2 0.3 - - - -
267D GLU* 5.9 1.0 - - - +
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Residues in contact with ILE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C LEU 5.1 0.2 - - - +
274C SER* 4.3 20.6 - - - +
277C ALA* 3.9 16.2 - - + -
296C TYR* 3.6 50.7 - - + +
300C VAL* 4.0 22.7 - - + -
304C HIS* 4.0 19.7 - - + +
329C ILE* 4.8 6.7 - - + -
338C ALA* 4.6 0.6 - - + +
339C TYR* 1.3 76.6 - - + +
341C PRO* 1.3 67.0 - - + +
343C ASN* 3.2 5.2 + - - +
344C VAL* 3.0 36.2 + - + +
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Residues in contact with PRO 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ILE* 3.7 22.9 - - + -
329C ILE* 4.2 16.6 - - + -
330C GLU 5.7 0.2 - - - +
331C THR* 3.8 26.2 - - + -
335C ASP 4.7 3.1 - - - +
336C VAL* 4.4 9.6 - - - +
338C ALA* 3.3 27.6 - - + +
340C ILE* 1.3 92.1 - - + +
342C THR* 1.3 56.4 + - - +
344C VAL* 4.2 1.1 - - + +
345C ILE* 2.9 39.1 + - + +
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Residues in contact with THR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ARG* 5.3 3.8 - - - +
336C VAL 3.1 16.5 + - - +
337C SER* 3.4 8.1 + - - -
338C ALA 2.6 24.4 + - - -
339C TYR* 4.1 6.7 - - - -
341C PRO* 1.3 73.7 - - - +
343C ASN* 1.3 67.0 + - - +
345C ILE* 5.0 3.1 - - - -
346C SER* 3.2 19.6 + - - -
159D ALA* 6.0 0.4 - - + -
311D TYR* 3.3 22.3 + - + +
313D PRO* 3.9 13.0 - - + -
314D ALA* 3.6 23.2 - - + +
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Residues in contact with ASN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C VAL* 3.6 16.6 - - - +
301C PHE* 3.2 53.2 - - + +
304C HIS* 4.9 4.9 - - + -
339C TYR* 2.9 54.2 + - - +
340C ILE* 3.7 5.7 - - - +
342C THR* 1.3 79.4 - - - +
344C VAL* 1.3 68.7 + - + +
346C SER* 3.6 5.0 + - - -
347C ILE* 3.6 7.3 - - + +
263D GLN* 3.3 13.2 + - - -
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 3.7 16.2 - - + -
273C LEU* 4.7 2.5 - - + -
304C HIS* 3.7 40.4 - - + +
308C LEU* 4.3 10.1 - - + -
329C ILE* 3.7 29.6 - - + -
340C ILE* 3.0 18.3 + - + +
341C PRO 3.2 1.1 + - - +
343C ASN* 1.3 75.3 - - - +
345C ILE* 1.3 60.0 + - - +
347C ILE* 2.8 22.6 + - - +
348C THR* 2.9 28.5 + - + -
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Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 3.7 19.3 - - + -
170C ILE* 3.7 20.9 - - + -
336C VAL* 4.6 14.8 - - + +
341C PRO* 2.9 24.1 + - + +
342C THR* 5.0 2.5 - - - -
344C VAL* 1.3 74.8 - - - +
346C SER* 1.3 62.9 + - - +
347C ILE 3.3 0.9 + - - -
348C THR* 3.4 21.8 + - - +
350C GLY 5.0 3.3 - - - +
351C GLN* 3.5 33.7 - - + +
375C ARG* 3.7 14.9 + - - +
159D ALA* 3.8 24.9 - - + +
337D ARG* 5.0 7.4 - - - +
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Residues in contact with SER 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PHE* 4.7 1.6 - - - -
342C THR 3.2 6.9 + - - -
343C ASN 3.6 10.7 + - - -
344C VAL 3.2 0.6 - - - -
345C ILE* 1.3 78.3 - - - +
347C ILE* 1.3 58.3 + - - +
159D ALA* 4.0 4.0 - - - +
190D ARG* 2.6 30.7 + - - +
222D MET* 4.4 3.6 - - - +
260D ARG* 3.3 29.6 + - - -
311D TYR* 2.9 41.6 + - - -
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Residues in contact with ILE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 4.3 4.2 + - - -
301C PHE* 3.6 29.6 - - + +
304C HIS* 3.8 15.7 - - + +
305C SER* 3.7 30.1 - - - +
308C LEU* 4.0 28.5 - - + +
309C GLU* 4.2 8.2 - - + +
343C ASN 3.6 12.1 - - - +
344C VAL* 2.8 10.7 + - - +
346C SER* 1.3 76.8 - - - +
348C THR* 1.3 67.4 + - + +
349C ASP* 3.8 2.3 + - - +
190D ARG* 3.5 20.8 + - - +
222D MET* 3.6 25.1 - - - -
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Residues in contact with THR 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 3.8 15.9 - - + +
167C GLU 5.0 0.2 - - - -
168C LEU* 3.4 24.8 - - + +
308C LEU* 3.7 28.5 - - + -
327C PRO* 4.2 7.0 - - + -
344C VAL* 2.9 24.3 + - + +
345C ILE* 3.4 12.0 + - - +
347C ILE* 1.3 78.8 - - - +
349C ASP* 1.3 59.9 + - - +
350C GLY 2.9 25.0 + - - -
375C ARG* 3.4 10.9 + - - -
190D ARG* 3.7 1.4 + - - -
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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
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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