Contacts of the helix formed by residues 307 - 324 (chain B) in PDB entry 4RN1
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 ASN 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A L8G 4.6 8.0 - - - -
271B GLY* 2.8 32.7 + - - +
272B ASP* 3.5 14.4 + - + +
273B PRO* 3.7 4.5 - - + +
306B TYR* 1.3 75.2 - - - +
308B LEU* 1.3 58.1 + - - +
309B ALA* 3.5 7.3 + - - +
310B ASN* 3.1 39.1 + - + +
311B THR* 2.8 33.0 + - - +
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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
----------------------------------------------------------
100A TYR* 5.6 7.6 - - + +
404A L8G 5.6 0.8 - - + -
33B LYS 5.3 0.9 - - - +
34B ILE* 4.3 12.3 - - + -
35B PRO* 3.3 38.8 - - + +
37B ARG* 3.6 38.4 - - + +
40B MET* 3.8 26.2 - - + +
305B GLY 4.2 4.7 - - - +
306B TYR 3.4 13.4 + - - +
307B ASN* 1.3 72.6 + - - +
309B ALA* 1.3 56.9 + - - +
311B THR* 3.4 4.4 + - - -
312B ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.9 13.1 - - + +
307B ASN* 3.3 7.0 + - - +
308B LEU* 1.3 78.4 - - - +
310B ASN* 1.3 58.7 + - - +
312B ALA 3.4 0.7 + - - -
313B ARG* 2.9 46.6 + - - +
339B ALA* 3.3 28.3 - - + +
340B TYR* 3.5 14.9 - - + -
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 5.6 0.7 - - - -
269B ILE* 4.6 8.7 - - + +
270B ALA 2.9 27.7 + - - -
271B GLY* 3.9 3.6 - - - -
272B ASP 5.9 0.2 - - - +
307B ASN* 3.1 38.0 + - + +
309B ALA* 1.3 73.9 - - - +
311B THR* 1.3 60.7 + - - +
313B ARG* 2.8 32.1 + - - +
314B CYS* 2.9 29.8 + - - +
348B ILE* 3.6 24.4 - - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 4.0 13.9 - - + -
41B VAL* 4.7 0.4 - - + -
266B ALA* 3.9 15.9 + - + +
272B ASP* 4.9 0.2 + - - -
305B GLY* 3.2 28.2 - - - +
306B TYR 3.8 0.3 + - - -
307B ASN 2.8 22.4 + - - -
308B LEU* 3.7 7.4 - - - -
310B ASN* 1.3 73.2 - - - +
312B ALA* 1.3 65.8 + - - +
314B CYS* 3.3 1.9 + - - +
315B TRP* 3.1 66.0 + - + +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 4.0 20.0 - - + +
41B VAL* 4.0 19.7 - - + +
44B LEU* 3.8 3.4 - - + -
308B LEU 3.0 17.7 + - - +
309B ALA 3.6 1.6 - - - +
311B THR* 1.3 75.1 - - - +
313B ARG* 1.3 65.0 + - - +
315B TRP* 4.5 0.3 - - - +
316B THR* 2.7 33.1 + - - -
340B TYR* 3.2 25.1 - - - +
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.0 7.8 - - - +
281B PRO* 4.6 2.1 - - + +
309B ALA* 2.9 33.4 + - - +
310B ASN* 2.8 37.0 + - - +
311B THR 3.3 0.2 - - - -
312B ALA* 1.3 76.6 - - - +
314B CYS* 1.3 61.5 + - - +
317B TYR* 3.1 24.4 + - - +
331B ILE* 4.7 0.2 - - + -
340B TYR* 2.8 53.4 + - + +
341B GLY 4.4 3.0 + - - -
343B ASP* 3.3 19.9 + - - -
345B VAL 2.8 20.4 + - - +
346B LEU* 3.4 38.1 - - + +
347B GLU 4.4 2.3 + - - -
348B ILE* 3.7 20.2 - - + -
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Residues in contact with CYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU 5.5 0.9 - - - -
266B ALA* 4.3 9.2 - - + -
269B ILE* 4.0 30.3 - - + -
281B PRO* 3.6 25.1 - - + +
284B ILE* 5.1 5.6 - - - -
310B ASN 2.9 16.8 + - - +
311B THR 3.6 4.9 - - - +
312B ALA 3.2 0.4 - - - -
313B ARG* 1.3 77.0 - - - +
315B TRP* 1.3 66.8 + - + +
317B TYR* 3.2 4.0 + - - +
318B LEU* 2.9 50.0 + - - +
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Residues in contact with TRP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.6 29.8 - - - -
41B VAL* 3.7 28.7 - - + -
45B ILE* 5.1 0.9 - - - -
137B TRP* 3.3 73.3 - + + +
264B LEU 2.9 22.0 + - - -
266B ALA* 3.9 7.0 - - + +
302B GLY* 3.6 13.9 - - - -
303B GLY 3.6 13.7 - - - -
304B GLY 3.6 13.7 - - - -
311B THR* 3.1 27.3 + - + +
312B ALA 4.5 0.2 - - - +
314B CYS* 1.3 86.5 - - - +
316B THR* 1.3 54.8 + - - +
318B LEU* 3.8 4.5 - - + -
319B THR* 2.6 37.9 + - - -
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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
----------------------------------------------------------
41B VAL* 4.0 2.8 + - - +
44B LEU* 3.4 27.1 - - + +
45B ILE* 3.6 18.1 - - - +
48B TYR* 3.7 32.1 - - + -
50B LEU* 3.6 12.6 - - + +
312B ALA 2.7 23.7 + - - -
313B ARG 4.0 2.0 - - - -
315B TRP* 1.3 76.4 - - - +
317B TYR* 1.3 63.7 + - - +
319B THR* 3.3 8.9 + - - -
320B GLY 3.1 16.1 + - - -
327B LEU* 3.6 10.1 - - + +
346B LEU* 4.9 1.8 - - + -
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO* 3.3 42.8 - - + -
282B VAL* 3.8 30.0 + - + +
285B GLY* 4.4 4.4 - - - -
289B LYS* 5.2 6.6 + - - -
313B ARG 3.1 18.7 + - - +
314B CYS 3.5 2.9 - - - +
316B THR* 1.3 77.7 - - - +
318B LEU* 1.3 62.9 + - + +
320B GLY* 3.0 4.9 + - - -
321B VAL* 2.9 47.7 + - + +
327B LEU* 4.2 12.5 - - + +
346B LEU* 4.5 20.6 - - + +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 4.0 10.3 - - + -
264B LEU* 3.8 28.7 - - + -
281B PRO 3.8 9.9 - - - +
284B ILE* 4.0 16.8 - - + -
285B GLY* 3.6 35.2 - - - +
288B LEU* 3.7 13.1 - - + +
314B CYS* 2.9 33.0 + - - +
315B TRP* 3.9 15.0 - - + +
316B THR 3.3 0.2 - - - -
317B TYR* 1.3 76.9 - - + +
319B THR* 1.3 60.5 + - - +
321B VAL* 3.2 5.7 + - + +
322B ILE* 3.0 34.4 + - - +
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.7 9.8 - - + +
50B LEU* 4.0 15.9 - - + -
54B MET* 3.9 36.1 - - + -
135B ILE* 4.7 6.5 - - + -
137B TRP* 3.1 19.4 + - - +
315B TRP 2.6 21.5 + - - -
316B THR* 3.4 9.4 - - - -
318B LEU* 1.3 77.2 - - - +
320B GLY* 1.3 56.3 + - - +
322B ILE* 3.3 10.6 + - - +
323B LEU* 3.0 31.5 + - + +
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.0 10.7 - - - +
316B THR 3.1 9.8 + - - -
317B TYR 3.0 8.4 + - - -
319B THR* 1.3 76.2 - - - +
321B VAL* 1.3 52.4 + - - +
323B LEU* 3.3 5.5 + - - -
324B GLY 2.7 28.8 + - - -
325B LYS* 2.7 29.2 + - - -
327B LEU* 4.7 8.1 - - - -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY* 4.1 7.9 - - - +
288B LEU* 3.8 19.1 - - + -
289B LYS* 3.6 42.1 - - + +
292B LEU* 4.5 5.6 - - + +
317B TYR* 2.9 49.3 + - + +
318B LEU* 3.4 11.7 - - - +
319B THR 3.2 0.2 - - - -
320B GLY* 1.3 74.0 - - - +
322B ILE* 1.3 65.9 + - - +
324B GLY* 3.1 13.9 + - - -
325B LYS 5.0 0.2 - - - -
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Residues in contact with ILE 322 (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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16B PRO* 4.3 19.9 - - + +
133B VAL* 4.0 24.5 - - + -
135B ILE* 3.7 25.1 - - + -
137B TRP* 4.8 2.7 - - + -
288B LEU* 3.8 18.2 - - + -
292B LEU* 4.0 18.6 - - + +
300B ILE* 4.0 29.6 - - + -
318B LEU 3.0 22.1 + - - +
319B THR* 3.5 9.4 - - - +
321B VAL* 1.3 75.6 - - - +
323B LEU* 1.3 62.6 + - + +
324B GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 3.6 31.0 - - + -
50B LEU* 3.6 48.0 - - + +
53B GLN* 3.7 29.7 - - + +
54B MET* 3.7 5.8 - - + -
319B THR* 3.0 27.1 + - + +
320B GLY* 3.8 4.0 - - - +
322B ILE* 1.3 76.6 - - + +
324B GLY* 1.3 61.9 + - - +
325B LYS* 3.4 20.9 + - + +
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Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLY 2.7 8.8 + - - -
321B VAL* 3.1 14.2 + - - -
322B ILE 3.2 0.6 - - - -
323B LEU* 1.3 78.9 - - - +
325B LYS* 1.3 61.3 + - - +
326B THR 4.2 0.7 + - - -
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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
------------------------------------------------------------
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