Contacts of the helix formed by residues 278 - 282 (chain A) in PDB entry 3QLE
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 ASP 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 5.0 3.6 - - - +
237A PHE* 5.1 2.8 - - - -
267A HIS 5.5 1.8 + - - -
268A CYS* 5.5 0.6 - - - +
269A VAL* 3.9 22.9 - - + +
276A ILE 3.3 3.8 + - - -
277A LYS* 1.3 69.1 - - - +
279A LEU* 1.3 58.5 + - - +
280A SER* 2.7 27.0 + - - -
281A LYS* 2.8 52.2 + - + +
282A LEU* 4.2 5.1 + - - +
301A LEU* 3.7 28.5 - - + +
302A GLN* 3.1 14.7 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.2 12.1 - - + -
237A PHE* 5.7 1.3 - - + -
277A LYS* 4.0 13.2 - - + +
278A ASP* 1.3 67.4 - - - +
280A SER* 1.3 56.8 + - - +
281A LYS 3.0 5.4 - - - -
282A LEU* 3.0 48.4 + - + +
283A ASN 4.6 0.3 + - - -
284A ARG 5.0 1.6 - - - +
286A LEU* 3.7 23.0 - - + +
289A VAL* 4.0 12.6 - - + -
291A ILE* 3.9 30.5 - - + -
299A TYR* 6.3 0.7 - - + -
302A GLN* 2.9 30.2 + - + +
305A ASN* 3.7 32.3 - - + -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 4.2 5.9 - - - +
278A ASP* 2.7 27.4 + - - -
279A LEU* 1.3 78.7 - - - +
281A LYS* 1.3 68.0 + - - +
282A LEU 3.3 0.8 + - - -
283A ASN* 4.4 4.1 + - - -
284A ARG 5.9 0.7 - - - -
286A LEU* 4.2 16.5 - - - +
302A GLN* 3.6 11.5 + - - +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 3.6 45.1 - - + +
177A PRO 4.0 17.7 - - - +
178A ASP* 3.4 13.3 - - - +
179A LEU* 2.7 45.3 + - + +
269A VAL* 4.8 2.4 - - - +
278A ASP* 2.8 45.0 + - + +
279A LEU 3.0 1.6 - - - -
280A SER* 1.3 88.7 + - - +
282A LEU* 1.3 57.7 + - - +
283A ASN 3.2 3.1 - - - -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 4.2 12.8 - - + -
180A LEU* 3.4 34.8 - - + +
193A THR* 5.4 1.3 - - + -
195A VAL* 3.6 32.8 - - + -
235A VAL* 5.1 1.6 - - + -
237A PHE* 4.8 6.7 - - + -
263A LEU* 3.7 29.8 - - + -
278A ASP 4.4 1.8 - - - +
279A LEU* 3.0 39.7 + - + +
281A LYS* 1.3 77.2 - - - +
283A ASN* 1.3 72.7 + - - +
284A ARG* 3.1 17.9 - - + +
289A VAL* 4.7 6.3 - - + -
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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