Contacts of the helix formed by residues 313 - 326 (chain B) in PDB entry 5IYB
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 GLU 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG 4.9 1.6 - - - -
279B VAL* 5.3 3.1 - - - +
311B ILE 2.8 18.4 + - - +
312B GLN* 1.3 75.9 - - - +
314B GLN* 1.3 65.3 + - - +
315B ASN* 3.4 18.1 - - - +
316B VAL* 3.2 21.9 - - + +
317B ALA* 3.2 5.2 + - - +
150S ALA* 5.5 3.5 - - - +
153S ARG* 2.3 35.0 + - - +
154S THR 5.5 1.2 + - - -
155S LEU* 3.9 28.2 + - + +
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Residues in contact with GLN 314 (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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274B ARG 3.7 15.8 + - - +
275B ALA 2.4 35.9 + - - +
276B LEU 3.3 3.8 + - - -
277B GLY* 3.1 27.8 - - - +
279B VAL* 5.3 5.2 - - + +
312B GLN 4.2 0.6 + - - -
313B GLU* 1.3 75.5 + - - +
315B ASN* 1.3 59.4 + - - +
317B ALA* 3.2 2.9 + - - +
318B LEU* 2.9 45.6 + - + +
358B GLU* 5.9 1.2 + - - -
111S LYS* 4.8 11.1 + - - -
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Residues in contact with ASN 315 (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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313B GLU* 3.6 21.0 - - - +
314B GLN* 1.3 80.8 + - - +
316B VAL* 1.3 84.7 + - - +
318B LEU* 3.2 13.7 + - - +
319B ASN* 2.9 22.0 + - - +
332B LYS* 4.8 9.9 - - - +
336B ILE* 3.6 24.7 - - + +
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Residues in contact with VAL 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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311B ILE* 4.1 15.4 - - + +
313B GLU* 3.2 26.0 - - + +
315B ASN* 1.3 91.0 - - - +
317B ALA* 1.3 59.6 + - - +
319B ASN* 3.1 8.5 + - - +
320B PHE* 2.7 34.4 + - - +
332B LYS* 4.5 13.2 - - - +
155S LEU 5.3 0.2 - - - +
156S THR 3.6 15.9 - - - +
157S ALA* 3.5 42.4 - - + +
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Residues in contact with ALA 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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271B ILE* 4.2 26.3 - - + +
274B ARG 4.6 1.8 - - - -
275B ALA 4.2 10.1 - - - +
311B ILE* 3.8 19.7 - - + +
313B GLU 3.2 16.3 + - - +
314B GLN* 3.4 5.6 - - - +
316B VAL* 1.3 80.5 - - - +
318B LEU* 1.3 62.2 + - - +
320B PHE* 3.4 6.2 - - - +
321B ILE* 3.1 29.3 + - - +
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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
----------------------------------------------------------
275B ALA* 3.7 27.4 - - + +
314B GLN* 2.9 37.0 + - + +
315B ASN* 3.3 9.4 - - - +
316B VAL 3.2 0.2 - - - -
317B ALA* 1.3 76.3 - - - +
319B ASN* 1.3 58.0 + - - +
321B ILE* 3.2 3.6 + - - +
322B GLY* 2.8 23.2 + - - -
335B ARG 4.7 0.2 - - - +
336B ILE* 3.7 29.6 - - + +
339B ALA* 3.3 25.0 - - + +
340B LYS* 4.4 20.4 - - + +
343B LEU* 4.0 16.4 - - + -
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Residues in contact with ASN 319 (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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315B ASN 2.9 14.0 + - - +
316B VAL* 3.1 11.4 + - - +
318B LEU* 1.3 76.7 - - - +
320B PHE* 1.3 57.9 + - - +
322B GLY* 3.2 2.7 + - - +
323B SER* 2.9 37.7 + - - -
332B LYS* 3.1 43.3 - - - +
335B ARG* 3.4 22.6 + - - +
336B ILE* 4.1 8.7 - - + +
158S GLU* 6.0 1.6 - - - +
162S GLU* 4.6 10.7 + - - -
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLU 6.1 0.2 - - - -
267B VAL* 4.0 13.0 - - + -
268B PRO* 4.8 4.7 - - + -
271B ILE* 3.6 38.4 - - + -
310B VAL* 6.4 1.1 - - + -
311B ILE* 4.4 16.6 - - + -
316B VAL 2.7 16.8 + - - +
317B ALA* 3.4 9.0 - - - +
319B ASN* 1.3 77.3 - - - +
321B ILE* 1.3 59.9 + - + +
323B SER* 3.5 1.6 + - - -
324B ARG* 3.1 78.3 + - + +
162S GLU* 4.1 29.2 - - + -
165S GLU* 4.2 20.4 - - + -
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Residues in contact with ILE 321 (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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260B LEU* 5.0 7.9 - - + -
263B ILE* 4.1 25.8 - - + +
267B VAL* 5.3 12.1 - - + -
271B ILE* 4.7 13.5 - - + +
272B VAL* 4.8 9.2 - - + -
275B ALA* 3.8 25.8 - - + -
317B ALA 3.1 16.0 + - - +
318B LEU* 3.2 10.1 + - - +
320B PHE* 1.3 77.3 - - + +
322B GLY* 1.3 62.9 + - - +
324B ARG* 3.4 7.1 + - - +
325B GLY* 3.1 19.8 + - - -
338B TYR* 5.3 1.0 - - + -
339B ALA* 4.4 13.2 - - + +
342B VAL* 6.0 1.3 - - + -
343B LEU* 3.8 23.3 - - + -
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Residues in contact with GLY 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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318B LEU 2.8 13.6 + - - -
319B ASN 3.2 4.0 + - - -
321B ILE* 1.3 78.4 - - - +
323B SER* 1.3 55.6 + - - +
326B ALA* 2.6 38.2 + - - +
335B ARG* 3.5 29.8 - - - -
338B TYR* 4.7 5.8 - - - -
339B ALA* 4.2 3.8 - - - +
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Residues in contact with SER 323 (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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319B ASN* 2.9 23.0 + - - -
320B PHE 4.0 1.8 - - - -
322B GLY* 1.3 73.9 - - - +
324B ARG* 1.3 69.5 + - - +
325B GLY 3.3 0.7 + - - -
326B ALA 4.1 8.9 - - - +
328B PRO* 6.2 0.2 - - - +
335B ARG* 2.3 38.5 + - - +
162S GLU* 3.8 22.5 + - - -
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Residues in contact with ARG 324 (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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263B ILE* 3.9 13.2 - - + -
264B LYS* 3.2 26.5 + - - +
265B GLN* 3.2 38.0 + - - +
266B GLU 5.4 2.7 + - - -
267B VAL* 4.0 22.0 - - + +
320B PHE* 3.1 56.5 + - + +
321B ILE 3.7 5.2 - - - +
322B GLY 3.3 0.2 - - - -
323B SER* 1.3 81.2 - - - +
325B GLY* 1.3 56.9 + - - +
162S GLU* 3.5 25.3 + - - +
165S GLU* 3.8 13.9 + - - -
166S ARG* 4.5 17.1 - - - +
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Residues in contact with GLY 325 (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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262B TYR 4.4 0.7 - - - -
263B ILE* 4.0 15.0 - - - -
264B LYS* 3.4 40.0 + - - +
321B ILE 3.1 9.9 + - - -
322B GLY 3.1 3.2 + - - -
323B SER 3.1 0.2 - - - -
324B ARG* 1.3 79.9 - - - +
326B ALA* 1.3 66.2 + - - +
338B TYR* 4.3 6.7 + - - -
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Residues in contact with ALA 326 (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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322B GLY 2.6 21.7 + - - +
323B SER* 4.1 8.3 - - - +
325B GLY* 1.3 78.5 - - - +
327B LYS* 1.3 71.6 + - - +
328B PRO* 3.7 5.0 - - - +
335B ARG* 4.7 8.7 - - + +
338B TYR* 3.3 35.6 - - + -
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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