Contacts of the helix formed by residues 397 - 407 (chain B) in PDB entry 2QUH
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 ASP 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B PHE 3.9 3.6 - - - -
378B SER* 3.4 6.2 + - - -
379B GLY* 2.8 22.7 + - - +
393B ASN 3.4 13.2 + - - +
394B CYS* 3.4 6.8 + - - +
396B VAL* 1.3 77.9 - - - +
398B VAL* 1.3 63.2 + - - +
399B SER* 2.9 33.5 + - - -
400B PHE* 2.9 16.5 + - + +
401B MET* 3.0 24.2 + - - +
420B TYR* 2.7 32.3 + - + -
427B THR* 4.9 0.5 - - - -
430B LEU* 3.4 10.2 - - - +
431B LYS* 5.8 1.8 - - - +
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Residues in contact with VAL 398 (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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341B PRO* 4.6 2.2 - - + -
342B ALA 3.8 8.7 - - - +
343B LEU* 3.7 19.3 - - + +
345B GLY* 3.7 32.8 - - - -
346B ALA 4.2 2.9 - - - +
376B ALA* 4.8 1.8 - - + -
377B PHE* 3.2 21.6 + - + +
396B VAL 3.3 4.2 + - - +
397B ASP* 1.3 69.3 - - - +
399B SER* 1.3 66.8 + - - +
401B MET* 3.1 11.7 + - - +
402B TYR* 3.0 60.0 + - + +
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL* 4.1 1.4 - - - +
376B ALA* 3.2 23.7 - - - +
377B PHE 4.1 1.4 + - - -
397B ASP* 2.9 10.3 + - - -
398B VAL* 1.3 79.6 - - - +
400B PHE* 1.3 62.1 + - - +
402B TYR* 3.4 4.7 + - - +
403B LEU* 3.3 22.7 + - - +
430B LEU* 4.0 18.6 - - - -
431B LYS* 3.6 20.0 - - - +
434B LEU* 3.7 24.7 - - - +
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Residues in contact with PHE 400 (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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394B CYS* 3.5 39.5 - - + +
397B ASP* 2.9 24.3 + - + +
399B SER* 1.3 74.1 - - - +
401B MET* 1.3 68.2 + - + +
403B LEU* 3.1 21.0 + - + +
404B THR* 3.1 23.6 + - - -
413B LEU* 4.0 29.6 - - + -
416B ILE* 4.1 16.6 - - + -
417B ARG* 3.6 45.8 - - + -
420B TYR* 5.7 0.4 - + - -
430B LEU* 4.1 9.6 - - + +
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Residues in contact with MET 401 (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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96B LYS* 4.2 7.9 - - - +
341B PRO* 4.0 23.8 - - + -
346B ALA* 3.9 30.7 - - + -
394B CYS 4.5 4.9 - - - +
395B ASP* 3.0 34.1 - - - +
396B VAL* 3.9 8.3 - - - -
397B ASP 3.0 13.8 + - - +
398B VAL* 3.1 16.6 + - - +
400B PHE* 1.3 78.4 - - + +
402B TYR* 1.3 62.3 + - + +
404B THR* 3.0 26.4 - - - -
405B PHE* 3.1 16.1 - - + -
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Residues in contact with TYR 402 (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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171B VAL* 6.1 0.4 - - + -
340B PHE* 3.6 31.6 - + + -
341B PRO* 2.7 38.0 + - + -
342B ALA 3.5 0.7 - - - -
343B LEU* 3.4 35.3 + - + +
350B MET* 3.3 11.2 - - + +
359B ILE* 4.1 12.1 - - + -
376B ALA* 6.0 0.2 - - + -
398B VAL* 3.0 32.3 + - + -
399B SER 3.6 3.4 - - - +
400B PHE 3.2 0.2 - - - -
401B MET* 1.3 76.3 - - + +
403B LEU* 1.3 66.1 + - - +
405B PHE* 3.1 9.2 + - - +
406B PHE* 3.0 27.4 + - + +
434B LEU* 3.5 33.9 - - + -
438B LEU* 4.3 11.7 - - + -
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Residues in contact with LEU 403 (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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134B ARG* 3.9 1.9 + - - -
399B SER 3.3 11.2 + - - +
400B PHE* 3.1 12.9 + - + +
402B TYR* 1.3 76.4 - - - +
404B THR* 1.3 61.7 + - - +
406B PHE* 5.0 0.4 - - - +
407B LEU* 2.7 43.1 + - + +
413B LEU* 3.7 15.0 - - + +
416B ILE* 3.9 30.1 - - + -
430B LEU* 3.6 27.8 - - + -
433B ALA* 4.6 3.8 - - + +
434B LEU* 3.7 32.3 - - + +
437B VAL* 4.1 19.3 - - + -
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Residues in contact with THR 404 (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 HIS* 4.2 1.0 - - - -
134B ARG* 2.9 47.1 + - + +
136B ILE* 3.7 23.9 - - + +
400B PHE* 3.1 28.4 + - - -
401B MET* 3.0 18.3 + - - +
403B LEU* 1.3 78.0 - - - +
405B PHE* 1.3 58.2 + - + +
413B LEU* 4.0 9.8 - - + +
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Residues in contact with PHE 405 (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 HIS* 3.3 21.4 + - - -
131B PHE* 3.4 9.9 - + - -
136B ILE* 3.4 42.8 - - + -
175B ILE* 3.4 31.2 - - + -
338B THR* 3.8 21.8 - - - -
339B PHE 4.0 10.8 - - - -
340B PHE* 3.7 36.1 - + + -
341B PRO* 3.9 13.5 - - + -
401B MET* 3.1 26.5 - - + -
402B TYR 3.1 6.7 + - - +
404B THR* 1.3 83.9 - - + +
406B PHE* 1.3 70.7 + - + +
407B LEU 3.9 0.2 - - - -
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Residues in contact with PHE 406 (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 HIS* 4.9 2.2 - - - -
171B VAL* 3.1 38.6 - - + -
174B LEU* 5.3 1.8 - - + -
175B ILE* 3.9 18.2 - - + -
178B ILE* 3.8 27.6 - - + -
340B PHE* 3.7 16.8 - + - -
402B TYR* 3.0 19.9 + - + +
403B LEU* 5.2 0.2 - - - -
405B PHE* 1.3 83.7 - - + +
407B LEU* 1.3 59.9 + - - +
408B GLU* 3.3 11.1 + - - +
434B LEU* 6.0 0.2 - - + -
437B VAL* 3.8 27.2 - - + +
438B LEU* 3.8 18.2 - - + -
441B LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 407 (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 HIS* 5.3 0.4 - - - -
134B ARG* 2.7 35.9 + - - -
403B LEU* 2.7 35.5 + - + +
405B PHE 3.9 0.2 - - - -
406B PHE* 1.3 70.7 - - - +
408B GLU* 1.3 59.6 + - - +
409B ASP* 4.1 14.1 - - + +
412B LYS* 4.1 23.1 - - + -
413B LEU* 3.7 37.9 - - + +
416B ILE* 4.0 20.0 - - + -
437B VAL* 4.1 20.2 - - + +
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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