Contacts of the helix formed by residues 333 - 348 (chain B) in PDB entry 4A8W
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 PRO 333 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASN* 4.6 0.4 - - - +
109B ARG* 3.7 24.9 - - - +
331B PHE 3.2 6.0 - - - +
332B TRP* 1.4 106.8 - - + +
334B GLY* 1.3 59.8 + - - +
335B TRP* 3.3 46.0 - - + +
336B LEU* 3.0 24.4 + - + +
405B LEU* 3.9 26.7 - - + -
485B TYR* 6.2 0.2 - - + -
486B MET* 4.5 0.4 - - - -
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Residues in contact with GLY 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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105B ASN* 4.8 4.0 + - - -
106B LEU* 5.8 3.5 - - - +
332B TRP* 3.7 6.7 + - - -
333B PRO* 1.3 68.3 - - - +
335B TRP* 1.4 63.9 + - - +
337B ARG* 3.1 39.0 + - - +
338B ASP* 3.1 11.0 + - - +
388B GLU* 3.2 27.8 + - - -
390B GLY* 5.8 0.6 - - - -
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Residues in contact with TRP 335 (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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106B LEU* 6.3 2.1 - - + +
109B ARG* 3.9 3.8 - - - +
115B ALA 3.0 20.0 + - - -
116B ASP* 3.2 30.7 - - - +
117B GLY* 3.3 11.6 - - - +
118B PRO* 3.9 27.6 - - + -
127B PHE* 3.8 28.7 - + - -
333B PRO* 3.3 33.8 - - + +
334B GLY* 1.4 76.3 - - - +
336B LEU* 1.4 77.7 + - + +
338B ASP* 3.4 10.1 + - - +
339B LEU* 2.9 32.3 + - + +
405B LEU* 5.1 2.0 - - + -
485B TYR* 3.6 30.7 - + + -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 3.8 27.1 - - + -
332B TRP* 3.9 15.9 - - + +
333B PRO* 3.0 21.8 + - + +
335B TRP* 1.4 91.4 - - + +
337B ARG* 1.3 55.1 + - - +
339B LEU* 3.2 9.8 + - + -
340B ILE* 2.8 59.2 + - + +
401B MET 4.4 0.7 - - - +
404B LEU* 4.2 6.5 - - + -
405B LEU* 3.5 47.6 - - + +
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B TRP* 3.6 29.5 - - + -
334B GLY* 3.1 22.6 + - - +
336B LEU* 1.3 75.8 - - - +
338B ASP* 1.4 90.1 + - - +
340B ILE* 3.4 6.1 + - - +
341B CYS* 3.0 35.5 + - - -
357B PHE* 5.8 0.7 - - - -
358B GLU* 3.6 24.5 - - - +
361B LEU* 3.1 50.2 + - + -
362B LYS* 3.5 23.7 - - - +
387B LEU 4.2 1.6 + - - -
388B GLU* 2.8 41.6 + - - +
390B GLY 5.9 0.2 + - - -
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Residues in contact with ASP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 3.1 6.8 + - - +
335B TRP* 3.8 10.2 - - - +
337B ARG* 1.4 113.7 + - - +
339B LEU* 1.3 58.7 + - - +
341B CYS* 3.5 5.4 + - - +
342B ASP* 3.0 29.5 + - - +
358B GLU* 4.4 12.6 - - - +
362B LYS* 5.0 3.8 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 3.7 24.5 - - + -
124B ASN* 3.6 21.5 - - - +
127B PHE* 3.8 33.4 - - + +
128B ARG* 3.8 34.3 + - + +
131B VAL* 4.6 2.9 - - + -
335B TRP* 2.9 22.6 + - + +
336B LEU* 3.2 12.8 + - + +
338B ASP* 1.3 72.3 - - - +
340B ILE* 1.4 63.5 + - - +
342B ASP* 3.3 7.2 + - - +
343B GLU* 2.9 26.9 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.8 29.5 - - + +
135B PHE* 4.6 10.1 - - + -
332B TRP* 4.5 1.3 - - + -
336B LEU* 2.8 49.5 + - + +
337B ARG* 3.7 5.8 - - - +
339B LEU* 1.4 70.3 - - + +
341B CYS* 1.3 57.5 + - - +
343B GLU* 3.3 3.3 + - - +
344B LEU* 2.9 46.5 + - + +
357B PHE* 4.2 16.2 - - + -
401B MET* 3.7 26.9 - - + -
404B LEU* 4.0 15.7 - - + -
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Residues in contact with CYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 3.0 22.4 + - - +
338B ASP* 3.8 6.5 - - - +
340B ILE* 1.3 74.7 - - - +
342B ASP* 1.3 62.2 + - - +
344B LEU* 3.3 3.8 + - - -
345B LEU* 3.1 31.3 + - + +
354B VAL* 3.5 24.8 - - + +
357B PHE* 4.0 14.4 - - - -
358B GLU* 3.6 47.6 - - + +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 2.9 34.1 + - - +
338B ASP 3.0 18.3 + - - +
339B LEU* 3.6 4.7 - - - +
341B CYS* 1.3 74.9 - - - +
343B GLU* 1.4 56.6 + - - +
345B LEU* 3.3 15.2 + - - +
346B ASN* 3.1 41.4 + - - +
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Residues in contact with GLU 343 (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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128B ARG* 2.8 69.5 + - + +
131B VAL* 3.9 15.7 - - + -
132B ARG* 2.7 41.6 + - + -
339B LEU 2.9 16.7 + - - +
340B ILE 3.8 3.8 - - - +
342B ASP* 1.4 73.7 - - - +
344B LEU* 1.4 58.3 + - - +
346B ASN* 3.1 15.6 + - - +
347B MET* 2.9 28.8 + - - +
429B MET* 4.3 5.8 - - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.8 11.9 - - + -
135B PHE* 3.6 41.3 - - + -
340B ILE* 2.9 35.9 + - + +
341B CYS* 3.7 7.9 - - - +
343B GLU* 1.4 73.9 - - - +
345B LEU* 1.4 61.6 + - - +
347B MET* 3.2 13.3 + - - +
348B GLY 3.3 0.2 + - - -
349B TYR* 3.0 44.9 + - + +
353B TRP* 3.9 26.7 - - + -
354B VAL* 3.9 15.0 - - + -
357B PHE* 4.8 7.2 - - + -
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Residues in contact with LEU 345 (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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341B CYS* 3.1 22.9 + - + +
342B ASP* 3.5 14.4 - - - +
343B GLU 3.3 0.2 - - - -
344B LEU* 1.4 76.1 - - - +
346B ASN* 1.4 62.9 + - - +
348B GLY* 3.1 15.6 + - - -
349B TYR 4.1 7.9 + - - +
351B PRO* 3.7 39.0 - - + +
354B VAL* 3.9 20.4 - - + -
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Residues in contact with ASN 346 (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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128B ARG* 3.8 2.2 - - - +
132B ARG* 4.2 9.5 + - - +
342B ASP* 3.1 31.5 + - - +
343B GLU* 3.1 35.7 + - - +
345B LEU* 1.4 75.4 - - - +
347B MET* 1.3 60.8 + - - +
348B GLY* 3.3 1.4 + - - -
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Residues in contact with MET 347 (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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131B VAL* 3.9 17.7 - - - +
132B ARG* 3.6 66.0 + - + +
135B PHE* 3.7 33.9 - - + +
136B SER* 4.0 7.2 - - - +
343B GLU 2.9 16.9 + - - +
344B LEU* 3.2 15.9 + - - +
346B ASN* 1.3 75.1 - - - +
348B GLY* 1.3 57.9 + - - +
349B TYR* 3.6 10.2 - - + -
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Residues in contact with GLY 348 (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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345B LEU 3.1 12.7 + - - -
346B ASN 3.2 1.9 - - - -
347B MET* 1.3 77.5 - - - +
349B TYR* 1.3 65.7 + - - +
350B ALA* 3.7 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