Contacts of the helix formed by residues 328 - 340 (chain B) in PDB entry 3CRL
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 TYR 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 5.2 4.0 - - + -
131B ALA* 3.7 27.0 + - + -
134B VAL* 4.0 18.0 - - - +
155B LEU* 5.0 1.6 - - + -
159B TYR* 3.7 23.3 - + - -
306B TYR* 3.4 55.2 + + - +
310B THR* 3.3 23.9 + - - +
326B PHE* 3.5 19.5 - + + -
327B GLY* 1.3 89.7 - - - +
329B GLY* 1.3 65.0 + - - +
330B LEU 3.3 2.7 - - - -
331B PRO* 3.4 7.0 - - - +
332B ILE* 3.2 45.1 + - + +
1001B ANP 3.2 2.5 + - - +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B HIS* 5.6 1.3 - - - -
251B GLU* 3.2 32.5 - - - +
255B ASN* 5.5 0.2 - - - -
328B TYR* 1.3 77.7 - - - +
330B LEU* 1.3 55.9 + - - +
332B ILE* 4.3 1.9 - - - +
333B SER* 2.6 37.2 + - - -
1001B ANP 3.2 15.9 + - - -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.1 19.7 - - + -
255B ASN* 3.6 18.2 - - - +
303B LEU* 3.8 21.5 - - + +
304B PHE* 4.0 15.8 - - + -
329B GLY* 1.3 71.0 - - - +
331B PRO* 1.4 69.2 - - + +
333B SER* 3.3 4.9 + - - -
334B ARG* 3.1 22.5 + - - +
344B LEU* 4.6 5.3 - - + +
346B LEU* 3.7 31.4 - - + -
1001B ANP 2.7 58.3 + - + +
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Residues in contact with PRO 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 4.8 2.0 - - - +
303B LEU 4.1 4.3 - - - +
304B PHE* 3.7 38.1 - - + +
305B SER 4.5 3.8 - - - +
306B TYR* 3.5 40.1 + - + +
327B GLY 4.2 5.4 - - - +
328B TYR* 3.4 18.4 - - - +
330B LEU* 1.4 93.3 - - + +
332B ILE* 1.3 59.9 + - - +
334B ARG* 3.3 7.3 - - + +
335B LEU* 3.2 24.8 + - - +
1001B ANP 3.7 4.3 - - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.8 33.0 - - + -
159B TYR* 4.5 22.9 - - + -
163B ILE* 5.3 4.3 - - + -
247B HIS* 3.6 15.7 - - + +
306B TYR* 4.8 2.7 - - + -
328B TYR* 3.2 39.6 + - + +
329B GLY* 4.3 1.3 - - - +
331B PRO* 1.3 76.6 - - - +
333B SER* 1.3 66.0 + - - +
334B ARG 3.1 1.6 - - - -
335B LEU* 3.0 12.4 + - + +
336B TYR* 3.0 45.4 + - + -
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B HIS* 3.8 4.4 - - - -
248B MET* 3.5 21.3 - - - +
251B GLU* 3.4 25.5 - - - +
252B LEU* 5.6 1.6 - - - -
329B GLY 2.6 24.6 + - - -
330B LEU* 3.8 4.0 - - - -
332B ILE* 1.3 76.0 - - - +
334B ARG* 1.3 61.8 + - - +
336B TYR* 3.2 13.0 + - - +
337B ALA* 3.0 20.4 + - - +
344B LEU* 3.8 20.4 - - - -
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Residues in contact with ARG 334 (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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152B GLN* 5.8 1.8 - - - +
156B ASP* 5.0 12.7 + - - -
304B PHE* 3.6 54.8 + - + +
330B LEU 3.1 12.2 + - - +
331B PRO* 3.3 11.2 - - - +
333B SER* 1.3 77.1 - - - +
335B LEU* 1.3 54.3 + - - +
337B ALA* 3.1 3.8 + - - +
338B LYS* 2.7 67.7 + - - +
343B ASP* 3.9 11.2 + - - +
344B LEU* 3.7 33.4 + - + +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.6 39.5 - - + +
159B TYR* 3.4 31.2 - - + -
160B LEU* 3.6 27.4 - - + +
163B ILE* 4.1 8.3 - - + -
306B TYR* 3.3 20.4 - - - +
331B PRO 3.3 12.1 - - - +
332B ILE* 3.0 15.1 + - + +
334B ARG* 1.3 77.0 - - + +
336B TYR* 1.3 65.3 + - - +
338B LYS* 3.0 12.1 + - + +
339B TYR* 2.9 25.5 + - - +
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Residues in contact with TYR 336 (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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162B ARG* 4.8 8.8 + - - -
163B ILE* 3.8 36.3 - - + +
166B ARG* 5.5 3.6 - - - -
240B TYR* 3.8 11.3 + - - -
244B HIS* 3.7 44.8 - + + +
247B HIS* 3.7 36.7 + + + -
248B MET* 3.9 19.7 - - + -
332B ILE* 3.0 45.6 + - + -
333B SER 3.5 6.7 - - - +
335B LEU* 1.3 78.1 - - - +
337B ALA* 1.3 62.0 + - - +
339B TYR* 3.3 16.1 + - - +
340B PHE* 4.3 0.3 + - - -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 4.6 3.2 + - - -
248B MET* 3.5 24.8 - - - -
333B SER 3.0 9.2 + - - +
334B ARG 3.1 7.6 + - - +
336B TYR* 1.3 76.6 - - - +
338B LYS* 1.3 59.9 + - - +
339B TYR 3.4 0.3 + - - -
340B PHE* 4.1 2.6 + - - +
342B GLY* 2.9 28.8 + - - -
343B ASP 3.5 30.1 - - - +
344B LEU* 3.9 5.2 - - + +
358B ILE* 4.3 4.0 - - + -
359B TYR 4.4 0.8 - - - +
360B LEU* 4.7 4.3 - - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 5.9 1.2 + - - -
160B LEU* 4.5 10.3 - - + -
334B ARG* 2.7 53.6 + - - +
335B LEU* 3.0 15.2 + - + +
337B ALA* 1.3 72.9 - - - +
339B TYR* 1.3 62.7 + - - +
340B PHE 3.3 0.4 - - - -
341B GLN* 3.2 12.2 + - - -
342B GLY 3.7 12.6 - - - +
343B ASP* 3.3 30.3 - - - +
370B ARG* 3.3 20.6 - - + +
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Residues in contact with TYR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.7 22.9 - - + -
163B ILE* 3.9 17.0 - - + -
164B SER* 3.4 27.4 - - - -
167B MET* 3.4 27.4 - - + +
244B HIS* 4.0 11.2 - + - -
335B LEU 2.9 11.3 + - - +
336B TYR* 3.4 15.0 - - - +
337B ALA 3.2 1.4 - - - -
338B LYS* 1.3 78.3 - - - +
340B PHE* 1.3 95.2 + + - +
341B GLN 3.4 0.2 - - - -
368B VAL 3.4 0.2 - - - +
369B GLU* 2.3 46.2 + - + +
370B ARG* 2.8 33.6 + - - -
371B LEU* 4.1 5.6 - - + -
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Residues in contact with PHE 340 (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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31B LEU 4.3 3.1 - - - -
33B MET* 3.8 31.0 - - + -
36B PHE* 4.5 8.1 - + - -
167B MET* 4.4 11.7 - - + -
240B TYR* 4.3 32.1 + + + +
241B VAL* 4.6 3.6 - - + -
244B HIS* 4.4 11.4 - + - -
336B TYR 4.3 1.4 + - - -
337B ALA 4.1 3.2 + - - +
338B LYS 3.3 0.2 - - - -
339B TYR* 1.3 118.0 - + + +
341B GLN* 1.3 71.3 + - - +
342B GLY* 3.3 3.3 + - - -
360B LEU* 6.1 1.4 - - + +
361B LYS* 3.8 14.2 + - - +
367B SER* 3.5 42.2 + - - +
368B VAL 3.7 5.8 - - - -
369B GLU* 4.2 14.8 - - + -
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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