Contacts of the helix formed by residues 368 - 377 (chain B) 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 ALA 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 4.0 7.0 - - - +
366B GLU 3.4 5.1 + - - +
367B ASP* 1.4 71.7 + - - +
369B PHE* 1.3 65.5 + - - +
370B ILE 3.2 3.1 - - - -
371B ALA* 3.0 16.6 + - - +
372B ASP* 3.7 6.7 + - - +
394B ALA* 3.6 30.1 - - + +
395B LYS* 4.1 11.0 - - - -
398B ARG* 3.7 19.3 - - + -
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 3.5 55.6 - - + -
118B ALA* 4.5 3.8 - - + -
119B ARG* 3.2 20.9 - - + +
129B LEU* 3.4 32.1 - - + -
133B LEU* 3.9 18.4 - - + -
333B PRO* 6.0 0.9 - - + -
339B ILE* 3.8 33.7 - - + -
367B ASP* 2.7 21.8 + - - +
368B ALA* 1.3 70.5 - - - +
370B ILE* 1.3 63.2 + - + +
372B ASP* 3.2 6.9 + - - +
373B PHE* 3.0 41.6 + + - -
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B MET* 6.4 0.4 - - - -
333B PRO* 4.2 22.9 - - + -
358B MET* 3.4 18.4 - - + +
359B SER* 3.8 14.4 - - - +
360B HIS* 3.6 32.5 - - - +
364B GLU* 4.8 4.0 - - - +
368B ALA 3.1 0.2 + - - -
369B PHE* 1.3 78.1 - - + +
371B ALA* 1.3 62.0 + - - +
373B PHE* 3.7 7.4 - - - -
374B ALA* 3.1 23.9 + - - +
382B ILE* 3.9 7.9 - - + +
384B THR* 3.7 25.1 - - - +
395B LYS* 3.9 23.3 - - + -
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA 3.0 11.4 + - - +
370B ILE* 1.3 80.0 - - - +
372B ASP* 1.3 65.7 + - - +
374B ALA* 3.4 1.6 + - - +
375B VAL* 3.3 26.5 + - - +
382B ILE* 4.2 7.0 - - - -
395B LYS* 3.6 31.2 - - + +
398B ARG* 3.8 16.2 - - + -
399B LEU* 3.7 17.5 - - + +
402B ILE* 4.4 1.3 - - - -
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 5.4 1.2 + - - -
129B LEU* 3.5 27.1 - - + +
130B TYR* 3.0 34.4 + - - +
133B LEU* 5.1 0.2 - - - -
368B ALA 3.7 6.3 + - - +
369B PHE 3.2 7.5 + - - +
371B ALA* 1.3 78.7 - - - +
373B PHE* 1.3 59.0 + - - +
375B VAL 3.2 0.5 + - - -
376B ALA* 2.8 31.3 + - - +
398B ARG* 2.8 50.3 + - - +
402B ILE* 4.1 4.3 - - - -
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.8 19.7 - - + +
333B PRO* 4.2 9.9 - - + -
339B ILE* 3.8 46.2 - - + -
342B THR* 3.7 25.4 - - + -
343B MET* 3.7 19.5 - - + -
358B MET* 3.7 23.9 - - + +
369B PHE* 3.0 30.9 + + + +
370B ILE* 3.9 7.0 - - - +
371B ALA 3.3 0.2 - - - -
372B ASP* 1.3 77.9 - - - +
374B ALA* 1.3 63.0 + - - +
376B ALA* 3.3 2.2 + - + -
377B LEU* 3.1 45.3 + - + +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE 4.4 2.9 - - - +
142B PRO* 4.2 20.6 - - + +
358B MET* 3.7 14.5 - - + +
370B ILE 3.1 18.1 + - - +
371B ALA 3.9 4.5 - - - +
373B PHE* 1.3 76.1 - - - +
375B VAL* 1.3 61.0 + - - +
378B ASN* 3.2 2.4 + - - -
379B THR* 2.9 50.9 + - - +
380B GLY 4.5 0.5 + - - -
381B GLN 4.5 0.4 - - - +
382B ILE* 4.4 5.6 - - + -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.9 26.5 - - + -
138B ALA* 3.6 4.7 - - - +
139B SER* 4.0 20.2 - - - +
140B ILE 3.8 22.4 - - - +
141B LEU* 4.1 9.4 - - + -
142B PRO* 4.2 2.5 - - + -
371B ALA 3.4 13.9 - - - +
372B ASP 3.2 5.1 + - - +
373B PHE 3.2 0.4 - - - -
374B ALA* 1.3 73.9 - - - +
376B ALA* 1.3 68.7 + - - +
378B ASN* 3.0 20.1 + - - +
399B LEU* 3.7 20.9 - - + -
402B ILE* 4.0 17.7 - - + -
406B SER* 5.4 0.7 - - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 3.6 18.6 - - - +
133B LEU* 3.5 33.7 - - + -
134B GLY* 3.4 18.9 - - - +
138B ALA* 3.8 8.0 - - - +
372B ASP 2.8 18.3 + - - +
373B PHE* 3.3 8.3 + - - +
375B VAL* 1.3 78.4 - - - +
377B LEU* 1.3 65.2 + - + +
378B ASN* 3.6 3.5 + - - -
137C ASN* 5.3 1.7 + - - -
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 4.8 0.4 - - - +
343B MET* 3.9 19.1 - - + +
346B VAL* 3.9 38.4 - - + -
350B GLN* 3.2 19.2 + - - +
358B MET* 4.3 8.1 - - + -
373B PHE* 3.1 41.4 + - + +
376B ALA* 1.3 82.8 - - + +
378B ASN* 1.3 72.4 + - - +
379B THR* 3.1 11.2 + - + -
137C ASN* 3.7 39.9 - - + +
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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