Contacts of the strand formed by residues 331 - 335 (chain B) in PDB entry 4LQL
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 GLU 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU* 2.5 30.7 - - - +
330B MET* 1.3 79.3 - - - +
332B ASP* 1.3 68.2 + - - +
333B TYR* 5.4 4.1 - - + -
346B GLY* 3.3 4.0 - - - -
347B SER 2.9 31.3 + - - +
348B HIS* 2.6 31.6 + - + +
446B HIS* 3.2 31.9 + - + +
447B HIS* 2.5 17.1 + - + -
128C HIS* 3.4 25.0 + - - +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 1.3 74.6 - - - +
333B TYR* 1.3 56.7 + - - +
344B ILE* 3.4 22.5 - - + +
346B GLY* 4.0 4.7 - - - -
426B TRP* 3.2 28.7 - - - -
446B HIS* 3.7 14.0 + - + +
448B THR* 4.8 3.5 + - - +
127C ALA* 4.0 17.9 - - + +
128C HIS* 2.7 37.7 + - + +
131C ARG* 2.9 32.4 + - - -
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.6 4.9 + - + -
332B ASP* 1.3 74.4 - - - +
334B THR* 1.3 67.4 + - + +
345B MET* 3.0 18.1 + - + +
346B GLY* 3.4 9.6 - - - -
347B SER* 3.9 29.6 - - - -
348B HIS* 4.1 4.3 - - - -
349B MET* 3.7 24.7 + - - -
419B LEU* 4.7 3.4 - - + -
421B VAL* 4.3 9.7 - - + +
423B LYS* 5.9 2.2 - - + -
118C MET* 3.5 30.7 - - - +
121C MET* 3.3 46.8 - - + +
124C HIS 4.4 6.2 - - - +
125C GLN* 4.5 7.6 - - + +
127C ALA* 3.4 15.5 + - - +
128C HIS* 4.2 19.4 + + - -
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Residues in contact with THR 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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333B TYR* 1.3 86.2 - - + +
335B LEU* 1.3 87.9 + - - +
344B ILE* 3.6 5.9 - - - +
345B MET* 2.8 42.1 + - + +
106C GLN* 2.8 29.2 + - - +
111C ILE* 5.6 8.5 - - + -
116C ILE* 5.3 8.1 - - + -
121C MET* 5.1 13.2 - - + -
124C HIS* 4.2 3.4 - - - -
127C ALA* 3.7 7.6 - - - -
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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
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334B THR* 1.3 102.5 + - - +
336B ASP* 1.3 65.7 + - - +
337B LEU* 4.0 10.3 - - + -
343B ALA 3.3 11.7 - - - +
344B ILE* 4.3 9.4 - - + -
345B MET* 5.2 2.2 - - - +
432B LEU* 3.7 24.9 - - + -
106C GLN* 3.5 14.9 + - + +
110C ASN 4.3 4.7 - - - +
111C ILE* 4.3 7.3 - - - +
127C ALA* 4.1 17.3 - - + -
131C ARG* 6.3 0.2 - - - +
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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