Contacts of the strand formed by residues 380 - 383 (chain C) in PDB entry 3QN3
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 GLY 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C ILE* 3.9 24.6 + - - +
141C LEU 4.8 0.2 - - - +
142C PRO* 3.5 10.4 - - - +
143C VAL* 2.9 25.6 + - - +
374C ALA 4.6 1.0 + - - -
378C ASN* 3.2 4.5 - - - +
379C THR* 1.3 75.8 + - - +
381C GLN* 1.3 65.5 + - - +
410C LEU* 5.4 4.9 - - - -
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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
----------------------------------------------------------
142C PRO* 3.5 4.4 - - - +
143C VAL* 3.3 13.0 - - + +
145C MET* 3.3 15.9 - - + +
167C MET* 3.8 13.0 - - + +
169C PHE* 5.6 4.7 - - + -
303C GLN* 2.8 44.4 + - - -
355C LYS* 3.6 20.4 - - - +
356C CYS 3.9 9.1 + - - +
357C VAL* 3.8 14.0 - - + +
358C MET* 3.2 13.4 + - - +
379C THR* 2.8 26.8 + - - +
380C GLY* 1.3 83.4 - - - +
382C ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 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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142C PRO* 3.7 18.4 - - + +
143C VAL 3.1 5.3 + - - -
144C PRO* 3.2 23.0 - - + +
145C MET* 2.8 31.5 + - - +
357C VAL* 4.1 3.8 - - - -
358C MET* 3.2 18.4 - - + +
370C ILE* 4.0 28.3 - - + +
371C ALA* 4.1 14.4 - - + -
374C ALA* 4.2 6.1 - - + -
381C GLN* 1.3 75.8 - - - +
383C LYS* 1.3 57.9 + - - +
384C THR* 4.2 29.4 - - + -
395C LYS* 5.1 0.9 - - + -
399C LEU* 4.2 17.5 - - + -
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Residues in contact with LYS 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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145C MET* 3.6 32.8 - - + +
147C ASN* 5.9 1.8 - - + -
163C GLU* 2.9 27.0 + - - +
165C MET* 3.6 22.0 - - - -
280C GLU* 2.8 36.5 + - - +
307C ASP* 4.9 0.4 + - - -
330C LEU* 3.6 10.1 - - + +
332C LYS* 5.6 1.9 - - - +
357C VAL* 3.9 9.8 - - + +
358C MET 2.7 9.9 + - - +
359C SER* 3.4 19.1 - - - +
360C HIS* 2.8 45.7 + - + +
382C ILE* 1.3 72.9 - - - +
384C THR* 1.3 62.3 + - - +
385C GLY 5.1 0.4 - - - +
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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