Contacts of the helix formed by residues 374 - 383 (chain V) in PDB entry 3MQT
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 ASN 374 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348V GLN* 2.9 35.4 + - - +
349V LEU 2.9 15.2 + - - +
351V LEU* 3.8 32.1 - - + +
372V GLU 3.7 1.8 + - - -
373V LEU* 1.3 69.0 - - - +
375V ILE* 1.3 64.0 + - - +
376V GLU* 3.6 7.6 + - - +
377V PHE* 3.1 32.6 + - + +
378V VAL* 3.2 16.9 + - - +
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Residues in contact with ILE 375 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V TYR* 4.4 16.4 - - - +
351V LEU* 5.5 0.2 - - - +
373V LEU* 3.1 22.7 + - + +
374V ASN* 1.3 72.0 + - - +
376V GLU* 1.3 65.8 + - + +
378V VAL* 3.2 8.2 + - - +
379V GLU* 3.0 44.4 + - - +
386V PHE* 4.1 25.8 - - + -
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Residues in contact with GLU 376 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374V ASN* 3.3 6.6 + - - +
375V ILE* 1.3 78.6 - - + +
377V PHE* 1.3 59.1 + - - +
379V GLU* 3.4 11.7 + - - +
380V GLN* 2.8 41.7 + - - +
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Residues in contact with PHE 377 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 4.9 0.2 - - + -
17V VAL* 4.5 3.1 - - + -
344V THR* 4.0 23.3 - - + -
345V LEU* 3.8 24.5 - - + -
348V GLN* 3.6 34.1 - - + -
349V LEU* 4.2 28.3 - - + -
374V ASN* 3.1 30.5 + - - +
376V GLU* 1.3 78.0 - - - +
378V VAL* 1.3 58.5 + - + +
380V GLN* 3.4 18.5 - - - +
381V VAL* 2.9 64.3 + - + +
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Residues in contact with VAL 378 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V ILE* 5.1 2.5 - - + -
15V VAL* 5.1 1.6 - - + -
28V ILE* 4.4 13.0 - - + -
349V LEU* 3.6 29.4 - - + -
373V LEU* 4.1 18.8 - - + -
374V ASN 3.2 14.1 + - - +
375V ILE* 3.2 7.6 + - - +
377V PHE* 1.3 74.3 - - - +
379V GLU* 1.3 60.7 + - - +
381V VAL* 3.8 6.3 - - - -
382V THR* 2.8 54.4 + - + +
386V PHE* 4.1 25.4 - - + -
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Residues in contact with GLU 379 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375V ILE* 3.0 30.7 + - - +
376V GLU* 3.8 11.6 - - - +
378V VAL* 1.3 73.9 - - - +
380V GLN* 1.3 62.9 + - - +
382V THR* 4.1 0.2 - - - -
383V GLY* 3.0 26.2 + - - -
384V HIS 3.5 13.0 - - - +
385V LYS* 4.2 5.8 - - - +
386V PHE* 3.1 44.6 + - + +
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Residues in contact with GLN 380 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376V GLU* 2.8 30.2 + - - +
377V PHE* 3.4 21.1 - - - +
379V GLU* 1.3 75.9 - - - +
381V VAL* 1.3 64.4 + - + +
383V GLY* 3.9 5.5 + - - -
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Residues in contact with VAL 381 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 3.9 27.4 - - + -
16V ASN 4.7 17.6 + - - +
17V VAL* 4.8 8.3 - - + -
377V PHE* 2.9 55.5 + - + +
378V VAL* 3.6 11.2 - - - +
380V GLN* 1.3 81.2 - - + +
382V THR* 1.3 67.4 + - + +
383V GLY 3.6 0.2 + - - -
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Residues in contact with THR 382 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V ILE* 3.8 17.9 - - + +
14V PRO 3.8 22.7 - - - +
15V VAL* 4.4 7.6 - - + -
378V VAL* 2.8 44.2 + - + +
381V VAL* 1.3 76.2 - - + +
383V GLY* 1.3 60.4 + - - +
384V HIS* 3.2 28.9 + - - +
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Residues in contact with GLY 383 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379V GLU 3.0 15.7 + - - +
380V GLN 3.9 4.7 + - - -
381V VAL 3.4 2.0 - - - -
382V THR* 1.3 75.8 - - - +
384V HIS* 1.3 61.2 + - - +
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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