Contacts of the helix formed by residues 304 - 317 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B PRO* 1.3 77.0 - - - +
305B THR* 1.3 65.9 + - - +
306B GLY* 3.7 4.8 + - - -
307B ALA* 3.2 14.9 + - - +
308B LEU* 3.0 20.3 + - - +
325B PHE* 5.7 0.3 - - - -
351B HIS* 3.5 26.0 + - - -
353B LEU* 4.8 7.3 - - - +
356B GLU* 2.8 35.0 + - - -
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 4.0 17.3 - - + -
179B ASN* 3.5 34.8 + - - +
198B GLY* 4.4 1.3 - - - -
199B PHE* 4.3 15.9 - - - +
200B THR* 4.5 15.8 - - - +
203B THR* 4.8 4.0 + - - +
230B ILE* 4.6 12.8 - - + +
303B PRO 3.8 0.4 + - - -
304B SER* 1.3 73.4 - - - +
306B GLY* 1.3 59.2 + - - +
308B LEU* 3.2 11.6 + - - +
309B MSE 2.8 28.5 + - + +
351B HIS* 5.1 1.6 + - - -
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.9 23.3 - - - +
179B ASN* 5.2 0.2 - - - +
304B SER* 3.2 5.6 + - - -
305B THR* 1.3 79.8 - - - +
307B ALA* 1.3 50.3 + - - +
309B MSE 3.3 1.2 + - - +
310B LEU 2.7 31.9 + - - -
325B PHE* 3.3 27.6 - - - -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.0 13.0 - - + -
303B PRO* 4.0 2.5 - - + -
304B SER* 3.2 23.4 + - - +
306B GLY* 1.3 75.1 - - - +
308B LEU* 1.3 56.5 + - - +
310B LEU* 3.8 0.2 - - - +
311B LEU* 2.9 38.4 + - - +
325B PHE* 4.0 2.0 - - - -
356B GLU* 3.5 20.6 - - - +
360B TRP* 3.6 26.2 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PRO* 5.9 2.2 - - + -
230B ILE* 4.1 31.9 - - + -
275B LEU* 4.2 17.5 - - + -
280B ILE* 4.4 22.0 - - + -
283B LEU* 3.9 22.1 - - + +
302B MSE 6.2 2.5 - - + -
303B PRO* 3.6 38.4 - - + +
304B SER 3.0 13.7 + - - +
305B THR* 3.5 13.0 - - - +
307B ALA* 1.3 75.3 - - - +
309B MSE 1.3 58.4 + - - +
311B LEU* 3.5 2.1 + - + +
312B THR* 2.8 35.0 + - - -
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Residues in contact with MSE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.3 6.3 - - + +
176B PHE* 3.7 24.5 - - + -
177B ARG 4.4 5.8 - - - +
178B LEU* 3.9 32.3 - - + -
198B GLY* 3.8 24.5 - - - +
228B ILE* 3.4 36.8 - - + -
230B ILE* 4.9 10.5 - - - -
275B LEU* 5.3 0.7 - - + -
305B THR* 2.8 20.0 + - - +
306B GLY 3.5 4.0 - - - +
308B LEU* 1.3 75.0 - - - +
310B LEU* 1.3 62.1 + - - +
312B THR* 3.3 28.5 + - + +
313B ALA* 3.0 21.7 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.0 11.4 - - + +
306B GLY 2.7 20.9 + - - +
307B ALA 3.8 2.9 - - - +
309B MSE 1.3 71.8 - - - +
311B LEU* 1.3 58.9 + - - +
313B ALA* 3.1 3.8 + - - +
314B LEU* 3.0 44.5 + - + +
320B VAL* 3.7 22.2 - - + -
322B ALA* 3.9 15.9 - - + -
325B PHE* 3.7 29.6 - - + -
360B TRP* 3.5 42.4 - - + -
369B LEU* 3.7 10.8 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 5.6 0.7 - - + -
279B PHE* 4.4 1.6 - - - -
283B LEU* 3.6 42.0 - - + -
287B PHE* 4.4 21.1 - - + -
288B LEU* 4.1 25.4 - - + -
307B ALA 2.9 21.9 + - - +
308B LEU* 5.4 0.7 - - + -
310B LEU* 1.3 73.0 - - - +
312B THR* 1.3 64.9 + - - +
314B LEU* 3.2 17.5 + - + +
315B HIS* 2.8 36.6 + - + -
359B LEU* 4.2 18.8 - - + -
360B TRP* 4.2 10.8 - - + -
363B LEU* 4.7 4.0 - - + -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 3.7 20.9 - - + -
137B LEU* 3.8 20.9 - - + -
176B PHE* 4.7 0.9 - - + -
275B LEU* 3.4 16.1 - - + +
279B PHE* 3.3 23.7 - - - -
308B LEU 2.8 27.6 + - - -
309B MSE 3.6 25.6 - - + +
310B LEU 3.3 0.2 - - - -
311B LEU* 1.3 71.8 - - - +
313B ALA* 1.3 61.4 + - - +
315B HIS* 3.2 9.0 + - - +
316B THR* 2.8 20.7 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B CYS* 4.6 0.9 - - + -
153B VAL* 3.7 26.0 - - + -
176B PHE* 3.9 19.9 - - + -
309B MSE 3.0 9.2 + - - +
310B LEU 3.4 9.0 - - - +
312B THR* 1.3 76.1 - - - +
314B LEU* 1.3 58.0 + - - +
316B THR* 3.0 7.7 + - - -
317B CYS* 2.8 41.5 + - - +
320B VAL* 3.8 10.5 - - + -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 4.2 3.5 + - - -
70B LEU* 3.2 29.8 - - + +
84B PHE* 4.3 20.3 - - + -
86B LEU* 4.8 1.0 - - - +
310B LEU* 3.0 46.1 + - + +
311B LEU* 3.2 16.8 + - + +
313B ALA* 1.3 76.6 - - - +
315B HIS* 1.3 65.1 + - + +
316B THR 3.7 0.2 + - - -
317B CYS 4.2 0.9 - - - +
320B VAL* 3.6 28.5 - - + -
360B TRP* 5.0 0.2 - - + -
363B LEU* 4.0 26.0 - - + -
368B ILE* 4.1 22.7 - - + +
369B LEU* 4.1 6.5 - - + -
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Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 3.7 3.6 + - - -
84B PHE* 3.5 30.2 - + - -
85B ASN 4.0 12.8 - - - -
86B LEU* 3.3 29.0 - - + +
88B ILE* 5.2 0.7 - - + -
90B VAL* 4.2 11.6 - - + +
279B PHE* 3.8 16.7 - + + -
282B TYR* 2.7 38.8 + + - -
283B LEU* 3.9 19.5 - - + -
287B PHE* 4.2 5.2 - + - -
311B LEU* 2.8 29.1 + - + +
312B THR 3.9 3.8 - - - +
313B ALA 3.1 1.2 - - - -
314B LEU* 1.3 79.6 - - + +
316B THR* 1.3 61.6 + - - +
317B CYS 3.9 0.2 - - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ARG* 4.5 4.3 - - - +
90B VAL* 4.1 21.5 - - + -
137B LEU* 4.4 22.6 - - + +
138B PHE* 3.6 31.2 - - - -
149B ILE* 4.0 9.9 - - - +
176B PHE* 4.5 1.0 - - - -
312B THR 2.8 20.9 + - - +
313B ALA* 3.5 8.3 + - - -
315B HIS* 1.3 84.2 - - - +
317B CYS* 1.3 65.6 + - - +
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Residues in contact with CYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ARG* 3.5 11.6 + - - -
70B LEU* 3.3 20.8 - - - +
138B PHE* 4.1 2.5 - - - -
149B ILE* 3.7 9.2 - - - +
151B CYS* 2.0 53.6 - - + -
176B PHE* 4.1 4.0 - - - -
313B ALA* 2.8 24.5 + - - +
316B THR* 1.3 89.1 - - - +
318B ASP* 1.3 65.5 + - - +
319B GLN 3.8 6.5 - - - +
320B VAL* 3.8 3.6 - - + -
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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
------------------------------------------------------------
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