Contacts of the helix formed by residues 401 - 412 (chain A) in PDB entry 1U7F
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A PRO* 4.1 10.5 - - + -
231A PHE* 2.7 37.5 + - - +
232A TRP 3.2 5.6 + - - +
233A CYS* 3.4 22.4 - - - +
234A SER* 4.2 9.6 + - - +
249A HIS* 5.5 2.2 - - - -
399A HIS* 4.1 5.4 - - - +
400A LEU* 1.3 69.6 - - - +
402A GLY* 1.3 71.3 + - - +
404A LEU* 3.2 4.8 + - - +
405A GLN* 2.8 22.2 + - - +
356B PRO* 3.3 34.8 - - + +
366B GLN* 5.4 0.2 + - - -
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PRO* 4.1 19.0 - - - +
232A TRP* 4.3 5.7 + - - +
298A TYR* 5.5 4.5 - - - -
401A ASN* 1.3 82.2 - - - +
403A PRO* 1.3 71.1 - - - +
405A GLN* 2.8 11.0 + - - +
406A TRP* 3.0 31.9 + - - -
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Residues in contact with PRO 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TRP 5.5 0.4 - - - +
298A TYR* 5.2 4.5 - - + +
343A PHE* 3.4 35.0 - - + -
345A ASN* 3.6 10.5 - - - +
348A PHE* 3.4 25.3 - - + -
370A CYS* 3.5 20.6 - - - -
400A LEU* 3.5 22.2 - - + +
402A GLY* 1.3 87.4 - - - +
404A LEU* 1.3 55.8 + - - +
406A TRP* 3.4 9.6 + - + +
407A LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A THR* 4.4 22.2 - - + +
370A CYS* 3.5 26.7 - - + -
371A THR* 5.9 1.6 - - + -
399A HIS* 4.3 22.2 - - + +
400A LEU 3.0 21.2 + - - +
401A ASN* 3.6 4.0 - - - +
402A GLY 3.2 0.2 - - - -
403A PRO* 1.3 75.8 - - - +
405A GLN* 1.3 57.0 + - - +
407A LEU* 3.3 2.0 + - + -
408A ASP* 2.9 24.3 + - - +
354B VAL* 3.3 24.8 - - + +
356B PRO* 3.5 21.8 - - + -
366B GLN* 3.7 31.6 - - + +
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLU 4.5 4.4 + - - -
229A PRO* 3.6 21.4 - - - +
401A ASN 2.8 11.2 + - - +
402A GLY 2.8 8.9 + - - +
404A LEU* 1.3 74.9 - - - +
406A TRP* 1.3 94.0 + - + +
408A ASP* 3.3 3.6 + - - +
409A LYS* 3.2 34.1 + - - +
355B ASP* 3.1 25.0 + - - +
356B PRO* 3.9 6.2 - - + +
357B SER* 3.3 26.9 + - - +
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Residues in contact with TRP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLU* 4.4 22.9 - - + -
229A PRO* 4.8 1.1 - - + -
345A ASN* 5.5 9.0 + - + +
348A PHE* 5.0 7.6 - + + -
349A ALA* 5.7 8.1 - - + -
352A LEU* 3.8 22.0 - - + +
402A GLY* 3.0 28.5 + - - -
403A PRO* 3.8 12.8 - - + +
405A GLN* 1.3 105.4 - - + +
407A LEU* 1.3 63.5 + - - +
409A LYS* 3.3 45.8 + - + +
410A VAL* 3.6 9.0 + - - +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PHE* 4.6 4.0 - - + -
352A LEU* 4.0 20.1 - - + +
363A VAL* 3.2 36.8 - - + +
364A TYR 4.8 0.2 - - - +
366A LEU* 3.6 26.5 - - + +
367A THR* 3.5 33.7 - - + -
370A CYS* 4.6 3.8 - - - -
403A PRO 3.0 14.1 + - - +
404A LEU* 3.3 9.4 - - + +
406A TRP* 1.3 75.7 - - - +
408A ASP* 1.3 66.5 + - - +
410A VAL* 3.0 5.7 + - - -
411A LEU* 2.9 28.2 + - + -
354B VAL* 4.0 6.3 - - + -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU 2.9 13.7 + - - +
405A GLN 3.4 10.0 - - - +
407A LEU* 1.3 74.7 - - - +
409A LYS* 1.3 61.9 + - - +
411A LEU* 2.7 24.3 + - - +
412A THR* 2.9 19.1 + - - +
353B TYR* 3.3 14.2 - - - +
354B VAL* 3.5 8.2 - - + +
355B ASP* 3.5 27.2 + - + +
361B ARG* 2.5 48.8 + - - -
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLN* 3.2 18.8 - - + +
406A TRP* 3.3 47.8 - - + +
407A LEU 3.3 0.2 - - - -
408A ASP* 1.3 81.8 - - - +
410A VAL* 1.3 62.8 + - + +
412A THR* 2.8 21.3 + - - -
413A GLN* 3.4 19.7 - - - +
355B ASP* 5.9 0.2 - - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LEU* 4.2 27.4 - - + -
356A VAL* 3.8 28.5 - - + -
363A VAL* 4.5 6.5 - - + -
406A TRP 3.6 10.1 + - - +
407A LEU 3.0 9.2 + - - +
409A LYS* 1.3 78.3 - - + +
411A LEU* 1.3 61.6 + - - +
413A GLN* 3.7 12.6 + - - +
414A MET* 2.9 31.2 + - + +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A PHE* 3.4 38.3 - - + -
363A VAL* 3.6 18.2 - - + -
364A TYR* 4.0 26.5 - - + +
407A LEU* 2.9 22.0 + - + +
408A ASP* 2.7 15.5 + - - +
410A VAL* 1.3 69.1 - - - +
412A THR* 1.3 53.1 + - - +
413A GLN 2.5 17.8 + - - -
414A MET* 2.8 15.9 + - + +
415A GLY 4.4 1.4 + - - +
352B GLY 5.4 0.2 - - - +
353B TYR* 3.6 26.1 - - + -
354B VAL* 3.6 36.8 - - + -
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASP* 2.9 25.7 + - - +
409A LYS* 2.8 25.5 + - - -
411A LEU* 1.3 73.0 - - - +
413A GLN* 1.3 62.4 + - - +
415A GLY 5.3 0.4 - - - -
353B TYR* 3.2 33.7 + - + -
361B ARG* 3.7 12.6 - - - +
385B LYS* 4.4 15.0 + - - +
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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