Contacts of the helix formed by residues 335 - 340 (chain B) in PDB entry 3QEL
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 LEU 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLN* 5.0 16.4 - - + +
122B PRO* 4.1 22.9 - - + -
142B MET* 3.6 14.8 - - + +
300B ILE* 5.6 4.3 - - + +
303B ALA* 3.8 35.7 - - + +
304B ALA* 4.1 9.4 - - + +
307B MET* 4.0 22.3 - - - -
314B ILE* 5.6 0.4 - - + -
315B PRO* 4.2 20.9 - - + +
333B ASN 3.1 0.8 + - - -
334B MET* 1.3 75.5 - - - +
336B ASN* 1.3 63.8 + - - +
337B ARG 3.2 0.7 - - - -
338B TYR* 3.1 10.7 + - + -
339B LEU* 2.9 30.2 + - + +
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Residues in contact with ASN 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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141B SER 3.0 21.3 + - - -
142B MET* 3.4 29.7 - - - +
144B PHE* 3.7 17.7 - - + -
333B ASN* 2.9 43.0 + - - +
335B LEU* 1.3 76.3 - - - +
337B ARG* 1.3 62.7 + - - +
338B TYR 3.1 1.0 + - - -
339B LEU* 3.9 5.3 - - - +
340B ILE* 3.2 30.7 + - + +
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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
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311B HIS* 4.7 11.1 + - - -
334B MET* 3.3 56.5 + - - +
336B ASN* 1.3 78.2 - - - +
338B TYR* 1.3 91.9 + - + +
340B ILE* 3.9 19.2 - - - +
341B ASN* 4.4 5.4 + - - +
311D HIS* 5.4 7.5 - - - +
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Residues in contact with TYR 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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303B ALA* 3.7 24.9 - - + +
306B ASP* 3.9 25.9 - - + +
307B MET* 3.3 37.9 - - + -
310B GLU* 3.1 22.5 + - - +
311B HIS* 3.0 30.8 + + - -
334B MET* 4.2 7.4 - - + -
335B LEU* 3.1 9.3 + - + +
337B ARG* 1.3 105.1 - - + +
339B LEU* 1.3 63.0 + - - +
340B ILE 2.9 6.1 + - - -
341B ASN* 3.1 14.2 + - - +
342B VAL* 3.5 14.4 - - - +
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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
----------------------------------------------------------
122B PRO* 3.6 34.8 - - + -
124B LEU* 5.3 4.7 - - + -
142B MET* 4.2 0.4 - - + -
144B PHE* 4.0 28.9 - - + -
299B ILE* 3.7 32.9 - - + +
300B ILE* 4.1 18.6 - - + +
303B ALA* 3.7 22.1 - - + +
335B LEU* 2.9 26.5 + - + +
336B ASN* 3.9 13.2 - - - +
338B TYR* 1.3 76.3 - - - +
340B ILE* 1.3 58.8 + - - +
341B ASN 3.6 0.5 + - - -
342B VAL* 4.4 2.9 + - - +
349B LEU 5.2 1.0 - - - +
351B PHE* 3.5 18.7 - - + -
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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
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144B PHE* 4.3 9.4 - - + -
336B ASN* 3.2 19.6 + - + +
337B ARG* 3.9 14.6 - - - +
338B TYR 2.9 0.2 - - - -
339B LEU* 1.3 78.4 - - - +
341B ASN* 1.3 67.0 + - + +
342B VAL 4.0 0.7 - - - -
350B SER* 3.0 6.2 - - - -
351B PHE* 3.0 48.6 + - + +
352B SER 3.8 7.6 - - - +
353B GLU* 3.8 32.3 - - + +
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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