Contacts of the helix formed by residues 377 - 382 (chain C) in PDB entry 4L28
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 377 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ARG* 6.4 0.4 - - - -
111C PHE* 3.7 20.9 - - - -
116C GLY* 3.4 11.7 + - - -
345C LEU* 3.4 12.6 - - - -
347C GLY 3.8 2.9 - - - -
376C ASP* 1.3 79.0 - - - +
378C VAL* 1.3 64.3 + - - +
379C ARG* 3.0 33.4 + - - +
380C ASN* 3.6 6.1 + - - +
381C TYR* 3.5 18.5 - - - -
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 5.4 1.8 - - + -
379A ARG* 4.2 11.7 - - - -
339C ILE* 3.6 26.0 - - + -
345C LEU* 3.2 32.8 + - + -
346C CYS 3.1 23.6 - - - +
377C SER* 1.3 70.2 - - - +
379C ARG* 1.3 66.9 + - - +
380C ASN 3.0 3.1 - - - -
381C TYR* 2.9 21.2 + - - -
382C MET* 3.1 31.5 + - + +
385C PHE* 4.4 7.6 - - + -
386C LEU* 4.7 7.4 - - + -
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Residues in contact with ARG 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.3 15.2 - - - +
377A SER* 6.4 0.4 - - - -
378A VAL* 4.0 12.8 - - - -
379A ARG* 4.5 17.3 - - + -
382A MET* 3.8 31.4 - - + +
115C GLY 2.4 34.8 + - - -
116C GLY* 3.9 8.9 - - - -
149C ASN* 5.6 0.8 + - - -
152C ILE* 4.1 12.3 - - - +
176C GLU* 3.6 11.5 - - + +
180C VAL* 3.6 21.4 - - - +
377C SER* 3.0 16.1 + - - +
378C VAL* 1.3 80.9 - - - +
380C ASN* 1.3 91.8 + - - +
381C TYR 3.3 0.7 + - - -
382C MET* 3.4 23.7 - - - +
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Residues in contact with ASN 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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116C GLY 5.8 0.6 + - - -
117C SER* 5.5 0.2 - - - -
149C ASN* 2.9 28.1 + - - -
152C ILE* 4.2 2.7 - - - +
174C SER* 2.7 30.7 + - - -
176C GLU* 3.6 10.6 - - - +
177C LYS* 3.8 31.1 + - + +
376C ASP* 3.3 17.8 + - - +
377C SER* 3.6 4.2 + - - +
378C VAL 3.0 0.8 - - - -
379C ARG* 1.3 107.5 + - - +
381C TYR* 1.3 77.4 + - + +
382C MET 3.7 1.1 - - - -
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Residues in contact with TYR 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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176C GLU* 4.2 1.6 - - - -
177C LYS* 4.0 10.2 + - - -
304C GLU* 3.7 46.4 + - + -
332C PHE* 6.3 1.3 - + - -
347C GLY* 3.7 13.9 - - - -
348C GLY* 4.1 7.0 + - - -
349C SER* 5.5 0.5 + - - -
376C ASP* 2.7 31.6 + - - -
377C SER 3.5 17.9 - - - -
378C VAL* 2.9 8.3 + - - +
380C ASN* 1.3 95.1 - - + +
382C MET* 1.3 64.0 + - - +
383C THR 3.2 3.4 - - - -
384C LYS* 3.1 24.3 + - + -
385C PHE* 3.5 36.1 - + + -
386C LEU* 3.5 15.8 + - - +
601C PLP 4.0 10.0 - - - +
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Residues in contact with MET 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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176A GLU* 4.4 19.3 - - + +
179A ASP* 3.9 17.4 - - - +
180A VAL* 4.2 9.9 - - + -
379A ARG* 3.7 30.1 - - - +
382A MET* 4.3 15.3 - - + -
383A THR* 6.6 0.2 - - + -
176C GLU* 3.1 12.1 + - + +
378C VAL* 3.1 40.6 + - + +
379C ARG* 3.4 17.5 - - - +
380C ASN 3.7 0.2 - - - -
381C TYR* 1.3 78.5 - - - +
383C THR* 1.3 63.9 + - + +
384C LYS 3.3 0.2 - - - -
386C LEU* 3.5 43.8 - - + +
387C SER* 4.0 4.3 + - - -
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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