Contacts of the strand formed by residues 377 - 384 (chain C) in PDB entry 4EEM
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 GLN 377 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376C TYR* 1.3 78.6 - - - +
378C VAL* 1.3 94.9 + - - +
379C LEU* 3.4 11.6 + - + +
392C VAL* 3.8 4.3 - - - -
393C ASP* 2.9 47.3 + - + +
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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
----------------------------------------------------------
234C GLU* 3.8 22.0 - - + +
237C LYS* 5.5 1.1 - - - +
376C TYR* 3.7 25.5 - - + -
377C GLN* 1.3 91.7 + - - +
379C LEU* 1.3 65.3 + - - +
380C ASP 4.1 4.9 - - - +
381C VAL* 3.7 30.5 - - + -
390C ILE* 4.0 17.5 - - + -
391C THR 3.7 6.1 - - - +
392C VAL* 4.3 2.7 - - + -
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Residues in contact with LEU 379 (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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217C ALA* 3.5 30.5 - - + -
377C GLN* 3.8 25.1 - - + +
378C VAL* 1.3 79.4 - - - +
380C ASP* 1.3 61.9 + - - +
391C THR* 2.8 23.6 + - + +
393C ASP* 4.4 13.7 - - + +
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Residues in contact with ASP 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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378C VAL* 3.9 0.8 - - - +
379C LEU* 1.3 82.8 - - - +
381C VAL* 1.3 66.1 + - - +
382C GLN* 2.8 43.2 + - - +
389C GLN* 3.5 1.0 + - - +
390C ILE* 3.7 1.7 - - - -
391C THR* 2.9 54.5 + - - +
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Residues in contact with VAL 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLU* 5.7 2.7 - - - +
378C VAL* 3.7 21.3 - - + -
380C ASP* 1.3 80.9 - - - +
382C GLN* 1.3 65.1 + - - +
383C ARG* 3.9 25.0 + - - +
388C THR* 3.8 25.4 - - + -
389C GLN 3.3 3.1 - - - +
390C ILE* 4.5 13.5 - - + -
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Residues in contact with GLN 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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380C ASP* 2.8 30.2 + - - +
381C VAL* 1.3 75.1 + - - +
383C ARG* 1.3 60.0 + - - +
384C TYR* 3.3 52.2 + - + +
388C THR* 3.3 7.4 - - - +
389C GLN* 2.9 40.8 + - + +
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Residues in contact with ARG 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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163C MET* 2.7 37.0 - - + +
164C GLY* 4.4 10.3 - - - +
166C ARG* 5.9 3.6 - - - +
212C TYR* 4.4 0.4 - - - -
238C ASP* 2.9 42.8 + - - -
381C VAL* 3.9 17.8 + - + +
382C GLN* 1.3 73.5 - - - +
384C TYR* 1.3 60.1 + - - +
385C PRO* 4.6 0.2 - - - +
387C TYR 4.3 2.0 - - - -
388C THR* 2.9 34.8 + - - +
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Residues in contact with TYR 384 (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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163C MET* 3.7 1.6 - - - -
164C GLY* 2.7 26.2 + - - -
382C GLN* 3.3 47.0 + - + +
383C ARG* 1.3 74.1 - - - +
385C PRO* 1.3 77.8 - - + +
386C LEU 3.1 1.3 + - - +
387C TYR* 2.9 68.4 + + + +
389C GLN* 4.1 15.8 + - + -
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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