Contacts of the strand formed by residues 377 - 383 (chain C) in PDB entry 4LCC
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 HIS 377 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C HIS* 2.9 29.2 + + + +
371C VAL 3.6 4.3 - - - -
372C GLU* 3.4 27.7 + - - +
375C GLY 4.2 12.4 + - - -
376C VAL* 1.3 77.6 - - - +
378C MET* 1.3 62.6 + - - +
379C VAL* 4.4 3.6 + - + +
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Residues in contact with MET 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C PRO* 5.5 4.0 - - + -
295C PRO* 3.7 43.3 - - + +
297C VAL* 5.2 7.4 - - + -
369C CYS 3.4 0.6 - - - +
370C HIS* 3.1 5.5 - - - -
371C VAL* 2.5 64.8 + - + +
373C HIS* 4.0 16.2 - - + +
376C VAL* 4.2 18.4 - - + +
377C HIS* 1.3 77.4 - - - +
379C VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C MET* 5.4 7.6 - - + -
368C SER* 3.6 28.5 - - - +
369C CYS 3.2 8.7 - - - +
370C HIS* 4.2 18.8 - - + +
377C HIS* 5.1 4.0 - - + +
378C MET* 1.3 82.1 - - - +
380C LEU* 1.3 64.6 + - - +
381C GLN* 4.3 2.9 - - + +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C VAL* 4.0 32.8 - - + +
298C ARG* 5.0 0.4 - - - -
299C VAL* 3.8 30.9 - - + +
327C TRP* 5.0 0.2 - - - -
368C SER* 3.1 4.5 - - - -
369C CYS* 2.7 41.9 + - + +
379C VAL* 1.3 74.5 - - - +
381C GLN* 1.3 80.2 + - - +
382C GLY* 3.3 2.0 + - - -
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Residues in contact with GLN 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ILE* 3.5 44.5 - - + +
367C TYR 3.8 0.4 - - - -
368C SER* 3.7 13.9 - - - -
379C VAL* 4.3 2.8 - - + -
380C LEU* 1.3 83.6 - - - +
382C GLY* 1.3 65.0 + - - +
383C PHE 5.1 1.0 - - - +
384C GLN* 5.1 2.1 - - - +
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Residues in contact with GLY 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C VAL* 4.2 16.4 - - - -
327C TRP* 4.7 2.6 - - - -
367C TYR 2.7 14.1 + - - -
368C SER* 4.1 0.6 - - - +
380C LEU* 3.3 6.7 + - - -
381C GLN* 1.3 75.3 - - - +
383C PHE* 1.3 88.1 + - - -
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Residues in contact with PHE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C VAL* 3.6 31.2 - - + -
300C ASN* 4.1 7.6 - - - -
301C HIS* 3.7 41.3 - + + -
311C LEU* 3.4 41.3 - - + -
327C TRP* 4.7 0.7 - + - -
366C ILE* 3.5 4.9 - - - +
367C TYR* 2.9 34.7 + - + +
381C GLN* 3.7 1.9 - - - +
382C GLY* 1.3 96.9 - - - +
384C GLN* 1.3 65.3 + - - +
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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