Contacts of the helix formed by residues 304 - 316 (chain C) in PDB entry 6B3I
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 SER 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C THR* 1.3 80.3 - - - +
305C GLY* 1.3 67.1 + - - +
307C PHE 3.6 0.2 + - - -
308C ARG* 3.4 24.3 + - - +
402C EDO 3.1 36.9 + - - -
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Residues in contact with GLY 305 (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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304C SER* 1.3 73.0 - - - +
306C ASP* 1.3 67.1 + - - -
308C ARG* 3.3 11.9 + - - +
309C LYS* 3.2 23.1 + - - +
402C EDO 5.1 0.9 - - - -
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Residues in contact with ASP 306 (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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34C GLU* 2.8 44.6 - - - +
38C ILE* 4.5 1.5 - - - +
72C LEU* 5.5 0.7 - - - +
76C PHE* 3.4 47.4 - - + +
304C SER 3.7 0.6 + - - -
305C GLY* 1.3 71.6 - - - +
307C PHE* 1.3 62.7 + - - +
309C LYS* 3.4 5.6 + - - +
310C LEU 3.3 17.3 + - - -
402C EDO 5.1 1.2 + - - -
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Residues in contact with PHE 307 (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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75C ASN* 3.4 21.5 - - + +
76C PHE* 4.0 14.5 - - - +
79C THR* 3.2 23.6 - - - -
265C GLU* 3.4 40.6 - - + -
268C LEU* 4.8 1.3 - - + -
269C ILE* 3.6 26.5 - - + -
303C THR* 3.7 12.8 - - + -
304C SER 3.6 0.8 + - - +
305C GLY 3.2 0.8 - - - -
306C ASP* 1.3 80.3 - - - +
308C ARG* 1.3 63.2 + - - +
310C LEU* 3.5 2.9 + - + +
311C LEU* 3.2 54.3 + - + +
402C EDO 3.6 29.9 + - - +
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Residues in contact with ARG 308 (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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299C VAL 4.2 1.6 - - - +
300C ARG* 2.9 37.5 + - + +
303C THR* 3.2 40.2 + - - +
304C SER* 3.4 23.6 + - - +
305C GLY* 3.3 12.9 + - - +
307C PHE* 1.3 80.2 - - - +
309C LYS* 1.3 63.0 + - - +
311C LEU* 3.3 3.1 + - - +
312C VAL* 3.0 41.8 + - + +
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Residues in contact with LYS 309 (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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31C GLY 5.2 2.2 - - - -
34C GLU* 6.2 1.3 - - + -
35C ALA* 4.0 28.5 - - - +
38C ILE* 3.6 25.4 - - + +
305C GLY 3.2 14.2 + - - +
306C ASP* 3.4 5.4 + - - +
308C ARG* 1.3 80.3 - - - +
310C LEU* 1.3 61.5 + - - +
312C VAL* 3.7 5.1 + - - +
313C ALA* 3.2 22.2 + - - +
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Residues in contact with LEU 310 (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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38C ILE* 3.9 34.0 - - + +
41C LEU* 4.5 7.2 - - + -
42C SER* 4.5 2.9 - - - -
76C PHE* 4.0 30.7 - - + +
79C THR* 3.6 37.2 - - + -
80C ALA* 4.2 8.7 - - + +
83C LEU* 4.4 11.7 - - + -
306C ASP 3.3 14.1 + - - +
307C PHE* 4.0 4.5 - - + +
308C ARG 3.2 0.4 - - - -
309C LYS* 1.3 77.6 - - - +
311C LEU* 1.3 66.3 + - + +
313C ALA* 3.2 1.7 + - - +
314C LEU* 3.0 30.7 + - + +
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Residues in contact with LEU 311 (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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79C THR* 4.3 10.1 - - + +
268C LEU* 4.4 19.7 - - + -
269C ILE* 5.1 6.1 - - + -
272C ILE* 4.4 21.5 - - + +
273C VAL* 6.4 0.2 - - + -
299C VAL* 3.7 27.4 - - + -
303C THR* 4.5 1.1 - - + -
307C PHE* 3.2 56.5 + - + +
308C ARG 3.8 0.9 - - - +
310C LEU* 1.3 79.3 - - + +
312C VAL* 1.3 62.6 + - - +
314C LEU* 3.1 29.7 + - + +
315C LEU* 3.2 19.9 + - - +
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Residues in contact with VAL 312 (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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296C SER* 3.8 19.2 + - - +
299C VAL* 4.4 11.0 - - + -
300C ARG* 3.7 49.8 - - + +
308C ARG* 3.0 27.0 + - + +
309C LYS* 4.1 5.6 - - - +
311C LEU* 1.3 74.4 - - - +
313C ALA* 1.3 63.4 + - - +
315C LEU* 3.2 14.4 + - - +
316C HIS* 3.2 13.4 + - - +
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Residues in contact with ALA 313 (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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38C ILE* 3.7 12.8 - - + -
42C SER* 3.3 24.5 - - - +
309C LYS 3.2 18.8 + - - +
310C LEU 3.5 5.4 - - - +
311C LEU 3.2 0.8 - - - -
312C VAL* 1.3 78.9 - - - +
314C LEU* 1.3 59.7 + - - +
315C LEU 3.2 0.3 + - - -
316C HIS* 3.1 33.9 + - - +
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Residues in contact with LEU 314 (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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41C LEU 4.0 2.7 - - - +
42C SER* 3.8 27.1 - - - +
49C ARG* 6.1 0.7 - - - +
79C THR* 4.1 17.5 - - + -
83C LEU* 3.9 39.0 - - + -
272C ILE* 4.2 25.1 - - + +
273C VAL* 4.8 3.4 - - + -
276C ALA* 6.4 2.5 - - + -
280C LEU* 3.9 17.5 - - + +
281C GLN* 5.6 1.6 + - - -
310C LEU* 3.0 21.2 + - + +
311C LEU* 3.1 14.5 + - + +
313C ALA* 1.3 74.9 - - - +
315C LEU* 1.3 59.7 + - - +
316C HIS* 4.3 8.7 + - - -
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Residues in contact with LEU 315 (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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272C ILE* 4.3 16.6 - - + -
280C LEU* 4.3 12.6 - - + -
281C GLN* 5.0 1.6 + - - +
284C LYS* 2.5 48.7 + - + +
295C LEU* 3.8 24.0 - - + -
296C SER* 3.7 40.8 - - - +
299C VAL* 3.7 22.2 - - + -
311C LEU 3.3 15.5 - - - +
312C VAL* 3.2 6.5 + - - +
313C ALA 3.1 1.2 - - - -
314C LEU* 1.3 81.8 - - + +
316C HIS* 1.3 64.1 + - - +
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Residues in contact with HIS 316 (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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42C SER* 3.1 28.3 + - - -
43C GLY* 5.0 3.1 - - - -
281C GLN* 5.8 4.9 + - - +
284C LYS* 3.8 8.8 + - - +
296C SER* 5.3 5.7 + - - -
312C VAL* 3.2 13.5 + - - +
313C ALA* 3.1 23.8 + - + +
314C LEU* 4.3 9.3 + - - -
315C LEU* 1.3 82.6 - - - +
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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