Contacts of the helix formed by residues 304 - 315 (chain C) in PDB entry 6APL
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 PRO* 1.3 75.7 - - - +
305C THR* 1.3 61.4 + - - +
306C GLY* 3.8 4.0 + - - -
307C ALA* 2.9 13.7 + - - +
308C LEU* 2.8 24.3 + - - +
325C PHE* 5.6 0.5 - - - -
351C HIS* 3.6 29.3 + - - -
353C LEU* 4.5 9.0 - - - +
356C GLU* 2.6 37.7 + - - -
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Residues in contact with THR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C LEU* 3.8 16.2 - - + -
179C ASN* 3.6 34.6 + - - +
198C GLY* 3.9 1.6 - - - -
199C PHE* 3.9 19.3 - - - +
200C THR* 4.2 19.9 + - - +
203C THR* 5.3 1.9 + - - -
230C ILE* 4.7 8.6 - - + +
302C MSE 5.4 1.9 - - - +
303C PRO 3.7 1.2 + - - -
304C SER* 1.3 72.0 - - - +
306C GLY* 1.3 58.9 + - - +
308C LEU* 3.0 15.0 + - + +
309C MSE 2.9 31.7 + - + +
351C HIS* 4.9 3.6 + - - -
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Residues in contact with GLY 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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155C GLY* 5.7 0.7 - - - -
178C LEU* 3.8 25.8 - - - +
179C ASN* 5.0 2.0 - - - +
304C SER* 3.2 6.1 + - - -
305C THR* 1.3 79.0 - - - +
307C ALA* 1.3 55.7 + - - +
309C MSE 4.0 0.7 - - - +
310C LEU* 3.0 23.9 + - - +
325C PHE* 3.2 28.3 - - - -
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Residues in contact with ALA 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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288C LEU* 4.1 5.6 - - + -
303C PRO* 4.0 10.3 - - + -
304C SER* 2.9 17.3 + - - +
306C GLY* 1.3 72.6 - - - +
308C LEU* 1.3 67.4 + - - +
310C LEU* 3.9 0.3 - - - +
311C LEU* 3.1 31.7 + - - +
325C PHE* 4.0 1.2 - - - -
356C GLU* 3.3 32.8 - - - +
360C TRP* 3.8 20.9 - - + -
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Residues in contact with LEU 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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230C ILE* 3.8 27.1 - - + -
275C LEU* 4.0 20.4 - - + +
280C ILE* 4.4 12.3 - - + -
283C LEU* 4.6 17.7 - - + +
302C MSE 3.6 27.8 - - + -
303C PRO* 3.6 39.3 - - + +
304C SER 2.8 8.4 + - - +
305C THR* 3.0 15.2 + - - +
307C ALA* 1.3 77.6 - - - +
309C MSE 1.3 59.1 + - + +
311C LEU* 3.9 1.4 - - + +
312C THR* 2.8 34.1 + - - -
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Residues in contact with MSE 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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153C VAL* 4.1 8.1 - - + +
176C PHE* 3.4 35.5 - - + -
177C ARG 4.1 5.2 - - - +
178C LEU* 3.6 33.0 - - + -
196C PHE* 4.1 5.2 - - + -
197C TYR 4.1 0.2 - - - -
198C GLY* 3.5 33.4 - - - +
228C ILE* 3.5 37.0 - - + -
230C ILE* 5.2 6.1 - - - -
275C LEU* 6.0 0.2 - - - -
305C THR* 2.9 20.3 + - + +
306C GLY 4.0 0.9 - - - +
308C LEU* 1.3 72.8 - - - +
310C LEU* 1.3 60.7 + - - +
312C THR* 3.3 6.8 + - - +
313C ALA* 2.8 29.1 + - - +
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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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153C VAL* 3.8 18.7 - - + +
306C GLY 3.0 17.0 + - - +
307C ALA 3.9 3.1 - - - +
308C LEU 3.4 0.2 - - - -
309C MSE 1.3 76.5 - - - +
311C LEU* 1.3 57.0 + - - +
313C ALA* 3.1 5.9 + - - +
314C LEU* 2.9 28.3 + - + +
320C VAL* 3.9 23.8 - - + -
322C ALA* 4.1 13.9 - - + -
325C PHE* 3.7 26.7 - - + -
360C TRP* 3.5 43.5 - - + -
369C LEU* 4.2 14.8 - - + -
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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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84C PHE* 5.4 0.4 - - + -
279C PHE* 4.6 1.1 - - - -
283C LEU* 3.6 44.9 - - + -
287C PHE* 4.5 19.7 - - + -
288C LEU* 4.4 21.8 - - + -
303C PRO* 5.8 0.4 - - + -
307C ALA* 3.1 19.7 + - + +
308C LEU* 5.3 1.6 - - + -
310C LEU* 1.3 73.1 - - - +
312C THR* 1.3 65.5 + - - +
314C LEU* 3.1 23.0 + - + +
315C HIS* 2.9 33.3 + - + +
359C LEU* 4.2 19.5 - - + -
360C TRP* 4.4 8.1 - - + -
363C LEU* 4.6 2.5 - - + -
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Residues in contact with THR 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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90C VAL* 3.9 18.6 - - + -
137C LEU* 4.0 23.6 - - + -
176C PHE* 4.5 7.9 - - + -
228C ILE* 5.0 6.7 - - + +
275C LEU* 3.7 14.8 - - + +
279C PHE* 3.5 24.3 - - - -
308C LEU 2.8 25.5 + - - -
309C MSE 3.3 10.6 + - - +
311C LEU* 1.3 77.2 - - - +
313C ALA* 1.3 61.2 + - - +
315C HIS* 3.1 9.2 + - - +
316C THR* 2.8 21.7 + - - +
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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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151C CYS* 4.6 0.4 - - + -
153C VAL* 3.5 28.5 - - + -
176C PHE* 3.9 18.4 - - + -
309C MSE 2.8 9.3 + - - +
310C LEU 3.4 9.0 - - - +
312C THR* 1.3 76.2 - - - +
314C LEU* 1.3 58.8 + - - +
316C THR* 3.7 6.3 - - - -
317C CYS* 2.9 40.3 + - - +
320C VAL* 3.3 12.6 - - + +
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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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67C ARG* 3.4 19.1 + - - -
70C LEU* 3.7 13.4 - - + +
74C ILE* 5.4 0.5 - - - +
84C PHE* 4.5 17.3 - - + -
86C LEU* 5.3 0.3 - - - +
310C LEU* 2.9 23.7 + - + +
311C LEU* 3.1 25.3 + - + +
313C ALA* 1.3 76.2 - - - +
315C HIS* 1.3 62.5 + - - +
316C THR 3.4 0.2 - - - -
317C CYS 4.6 0.4 - - - -
320C VAL* 3.6 25.1 - - + -
360C TRP* 5.4 0.7 - - + -
363C LEU* 3.7 30.5 - - + -
368C ILE* 3.6 37.9 - - + +
369C LEU* 4.3 4.0 - - + -
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Residues in contact with HIS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 4.4 12.5 + - - +
84C PHE* 3.5 27.7 - + - -
85C ASN 3.9 17.0 - - - -
86C LEU* 4.5 16.2 - - + +
88C ILE* 4.1 3.1 - - + -
90C VAL* 4.2 18.0 - - + +
279C PHE* 3.9 16.2 - + + -
282C TYR* 2.6 40.4 + + - -
283C LEU* 4.0 12.3 - - + -
287C PHE* 4.5 2.9 - + - -
311C LEU* 2.9 29.8 + - + +
312C THR 3.1 5.1 + - - +
314C LEU* 1.3 77.9 - - - +
316C THR* 1.3 62.2 + - - +
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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