Contacts of the helix formed by residues 336 - 342 (chain B) in PDB entry 6U37
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 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B ASP* 3.5 13.0 + - - -
334B GLU 3.5 0.6 - - - -
335B GLY* 1.3 76.7 - - - +
337B TYR* 1.3 65.3 + - - +
338B PHE 3.4 0.2 + - - -
339B LEU* 3.4 21.3 + - - +
399B SER* 3.3 17.7 + - - -
442B TRP* 4.1 10.3 - - - -
443B MET* 2.9 60.1 + - - +
446B PRO* 4.0 4.3 - - - +
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Residues in contact with TYR 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 5.2 0.5 + - - -
82B GLY 4.7 3.6 - - - -
83B THR* 4.7 2.8 - - - +
86B TRP* 4.5 9.1 - - - -
334B GLU 4.5 1.0 + - - -
335B GLY 3.3 0.4 - - - -
336B SER* 1.3 82.9 + - - +
338B PHE* 1.3 93.6 + + + +
340B VAL* 3.4 22.3 - - - +
341B TYR* 3.3 33.8 + + - -
439B TRP* 3.3 46.0 - + - -
443B MET* 4.2 7.9 - - - -
446B PRO* 4.3 14.8 - - + -
447B HIS* 4.4 11.4 - - + +
449B TYR* 4.8 10.3 - + - -
601B VX 4.9 2.0 - - + -
602B PQV 4.6 5.3 - - + +
603B GOL 3.6 31.7 + - - -
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Residues in contact with PHE 338 (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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294B VAL* 3.3 26.8 - - + +
295B PHE* 3.4 43.1 - + + -
334B GLU 3.1 28.3 - - - -
335B GLY* 3.3 10.0 + - - +
336B SER 3.2 0.8 - - - -
337B TYR* 1.3 87.6 - + - +
339B LEU* 1.3 64.3 + - - +
340B VAL 3.4 0.7 - - - -
341B TYR* 3.4 13.2 + - - +
402B VAL* 4.3 11.9 - - + -
447B HIS* 3.6 34.8 - + + -
601B VX 3.9 24.9 - - + -
602B PQV 3.4 27.6 - - + -
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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
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294B VAL* 5.1 2.7 - - + -
335B GLY 3.3 11.9 - - - +
336B SER* 3.8 11.9 - - - +
337B TYR 3.3 1.6 - - - -
338B PHE* 1.3 75.8 - - - +
340B VAL* 1.3 58.2 + - - +
341B TYR 3.0 5.6 + - - -
343B ALA* 3.1 34.5 + - + +
346B PHE* 3.5 48.1 - - + +
395B ARG 4.3 1.1 - - - +
398B LEU* 4.0 18.6 - - + +
399B SER* 3.7 32.3 - - - +
402B VAL* 3.7 30.7 - - + -
442B TRP* 4.6 3.1 - - + -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.3 24.6 - - + +
77B TYR* 3.9 18.4 + - + +
336B SER 4.5 0.2 + - - -
337B TYR 3.4 18.6 - - - +
339B LEU* 1.3 74.9 - - - +
341B TYR* 1.3 71.0 + - + +
342B GLY 3.5 2.3 + - - -
343B ALA 5.5 0.4 - - - -
346B PHE* 4.3 8.9 - - + +
347B SER* 4.0 13.0 - - - +
348B LYS* 3.8 22.9 - - - +
439B TRP* 4.4 4.0 - - + -
442B TRP* 4.2 7.9 - - + -
443B MET* 3.7 28.0 - - + -
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Residues in contact with TYR 341 (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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74B ASP* 2.9 36.0 + - - -
76B LEU* 3.5 30.0 - - + +
83B THR* 3.7 11.1 - - - +
293B SER 4.3 2.3 - - - +
294B VAL* 3.5 11.2 - - + +
337B TYR* 3.3 54.0 + + - -
338B PHE* 3.6 10.5 - - - +
339B LEU 3.0 1.8 - - - -
340B VAL* 1.3 86.0 - - + +
342B GLY* 1.3 55.4 + - - +
439B TRP* 5.0 1.6 - + - -
602B PQV 3.4 69.0 - - + +
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Residues in contact with GLY 342 (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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292B GLU* 5.9 2.5 - - - -
293B SER 5.3 1.1 - - - -
294B VAL* 3.8 5.8 - - - +
340B VAL 3.5 3.2 + - - -
341B TYR* 1.3 80.4 - - - +
343B ALA* 1.3 66.2 + - - +
344B PRO* 3.4 7.8 - - - +
365B VAL* 4.1 16.8 - - - +
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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