Contacts of the helix formed by residues 312 - 325 (chain B) in PDB entry 4I5L
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 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B TYR* 4.3 0.9 - - - -
265B VAL* 5.5 0.3 - - - +
268B ARG* 3.7 16.3 + - - -
304B ILE 3.8 9.4 - - - -
305B ASN* 3.8 6.9 + - - -
307B LEU 3.1 19.0 + - - -
308B THR* 4.1 10.7 - - - +
310B PHE 3.5 2.5 - - - +
311B PHE* 1.3 74.8 - - - +
313B TYR* 1.3 63.0 + - - +
314B GLU* 3.5 10.7 + - - +
315B HIS* 2.9 27.5 + - - +
316B PHE* 3.2 18.2 + - - +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLY 5.3 0.2 - - - +
248B LEU* 3.9 19.7 - - + -
250B PHE* 3.6 38.6 - + + -
251B LEU* 3.9 13.3 - - + +
257B PHE* 3.5 24.6 - - - -
261B TYR* 4.0 8.3 - + - -
304B ILE* 4.0 19.0 - - + +
305B ASN* 2.9 15.2 + - - +
311B PHE 3.1 5.8 + - - -
312B SER* 1.3 72.5 - - - +
314B GLU* 1.3 64.0 + - + +
316B PHE* 3.0 29.5 + + - +
317B TYR* 2.9 44.9 + + + -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ASN* 2.8 42.8 + - - +
308B THR* 5.9 1.6 - - - +
312B SER* 3.7 7.7 + - - +
313B TYR* 1.3 77.3 - - + +
315B HIS* 1.3 66.6 + - + +
317B TYR* 3.3 8.2 + - - +
318B VAL* 3.1 30.5 + - + +
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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
----------------------------------------------------------
268B ARG* 3.5 33.7 + - - +
308B THR* 4.4 4.4 + - - -
312B SER* 2.9 25.8 + - - +
314B GLU* 1.3 78.1 - - + +
316B PHE* 1.3 63.9 + - - +
318B VAL* 3.6 5.5 + - + +
319B ILE* 3.1 39.8 + - + +
382B ILE* 4.7 7.4 - - + +
385B GLU* 3.0 32.3 + - - -
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 3.8 31.2 - + - -
260B ARG* 3.5 18.2 - - + -
261B TYR* 3.4 49.8 - + + -
264B THR* 3.3 34.8 - - + -
265B VAL* 5.7 1.1 - - + -
268B ARG* 5.7 1.2 - - - +
312B SER 3.2 10.7 + - - +
313B TYR* 3.0 38.4 + + - +
315B HIS* 1.3 77.3 - - - +
317B TYR* 1.3 65.5 + - - +
319B ILE* 3.1 3.1 + - - +
320B TYR* 2.8 52.2 + + + +
374B TYR* 4.0 0.9 - - - -
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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
----------------------------------------------------------
257B PHE* 3.5 35.3 - + - -
313B TYR* 2.9 34.9 + + + +
314B GLU* 3.6 10.5 - - - +
315B HIS 3.3 0.2 - - - -
316B PHE* 1.3 78.3 - - - +
318B VAL* 1.3 72.7 + - + +
320B TYR* 3.4 2.1 + - - +
321B CYS* 2.9 52.1 + - - -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.1 18.2 + - + +
315B HIS* 3.8 8.7 - - + +
317B TYR* 1.3 80.4 - - + +
319B ILE* 1.3 64.8 + - + +
321B CYS* 3.3 5.0 + - - +
322B LYS* 3.1 43.3 + - + +
381B LEU* 5.4 1.1 - - + -
385B GLU* 4.1 19.3 - - - +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 3.9 18.4 - - + -
268B ARG* 4.5 4.0 - - - -
315B HIS* 3.1 42.2 + - + +
316B PHE* 3.1 8.3 + - - +
318B VAL* 1.3 77.1 - - - +
320B TYR* 1.3 62.7 + - - +
322B LYS* 3.4 4.2 + - - +
323B PHE* 3.2 16.8 + - - +
374B TYR* 3.8 15.9 - - + +
377B PHE* 3.8 5.7 - - + -
378B VAL* 3.9 24.0 - - + -
381B LEU* 3.7 25.6 - - + -
382B ILE* 4.2 22.4 - - + -
385B GLU* 4.8 3.6 - - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 2.3 39.3 + - - +
257B PHE* 3.6 38.1 - + + -
260B ARG* 3.5 31.7 + - + +
316B PHE* 2.8 40.5 + + + +
317B TYR* 4.0 3.1 - - - +
319B ILE* 1.3 73.7 - - - +
321B CYS* 1.3 60.2 + - - +
323B PHE* 3.1 18.8 + + - +
324B TRP* 2.7 46.7 + + + +
330B HIS* 5.7 1.0 - - - -
332B LEU* 5.3 3.4 - - + +
374B TYR* 3.7 21.8 - + - +
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Residues in contact with CYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 5.7 2.5 - - - -
317B TYR* 2.9 58.8 + - - +
318B VAL* 3.8 4.7 - - - +
320B TYR* 1.3 78.7 - - - +
322B LYS* 1.3 63.7 + - + +
324B TRP* 3.6 11.9 - - + +
325B GLU* 3.0 34.1 + - - +
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Residues in contact with LYS 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 VAL* 3.1 34.5 + - + +
319B ILE 3.6 7.2 - - - +
321B CYS* 1.3 77.0 - - + +
323B PHE* 1.3 61.4 + - - +
325B GLU* 3.6 25.0 + - - +
326B LEU* 3.3 23.0 - - - +
342B HIS* 4.5 16.3 + - + +
343B ASN* 4.4 14.1 + - - +
377B PHE* 3.9 7.4 - - + -
381B LEU* 3.6 26.2 - - + -
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE 3.2 4.9 + - - +
320B TYR* 3.1 17.5 + + - +
322B LYS* 1.3 75.8 - - - +
324B TRP* 1.3 69.6 + - - +
326B LEU* 2.8 17.0 + - - +
327B ASP* 3.0 35.8 + - + -
332B LEU* 3.7 43.3 - - + -
333B LEU 4.0 0.9 - - - -
334B ILE* 4.0 24.0 - - + -
373B SER 4.4 1.3 - - - -
374B TYR* 3.4 41.7 - + + -
377B PHE* 3.5 42.1 - + + -
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Residues in contact with TRP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 4.2 7.9 + - - -
257B PHE* 6.3 0.4 - + - -
320B TYR* 2.7 45.4 + + + +
321B CYS* 3.2 12.5 + - + +
323B PHE* 1.3 80.9 - - - +
325B GLU* 1.3 78.0 + - + +
326B LEU 3.3 0.7 + - - -
327B ASP* 3.4 11.7 + - - +
328B THR* 4.8 0.9 - - - +
330B HIS* 3.1 50.7 + + - -
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Residues in contact with GLU 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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321B CYS* 3.0 21.2 + - - +
322B LYS* 3.6 32.6 + - - +
323B PHE 3.0 0.4 + - - -
324B TRP* 1.3 94.2 - - + +
326B LEU* 1.3 68.1 + - + +
328B THR* 3.7 15.4 - - - +
341B ARG* 5.2 1.2 + - - -
342B HIS* 6.0 0.2 + - - -
343B ASN 5.8 1.7 + - - -
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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
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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