Contacts of the strand formed by residues 407 - 412 (chain B) in PDB entry 3U7U
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 LEU 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 3.6 6.6 - - - +
403B LEU* 3.5 9.1 - - - +
404B TYR* 2.9 38.0 + - + +
405B SER* 3.8 12.1 - - - +
406B GLY* 1.4 77.9 - - - +
408B SER* 1.4 58.8 + - - +
409B LEU 4.6 0.2 - - - +
410B LEU* 3.7 29.7 - - + +
432B ASN* 3.4 32.5 - - + +
433B ILE 4.2 2.0 - - - +
434B TYR* 3.7 42.0 - - + -
459B ARG* 6.2 1.1 - - - +
461B VAL* 5.4 4.0 - - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 3.4 10.7 - - - +
377B LEU* 2.9 26.4 + - - +
398B ILE* 3.5 24.8 - - - +
400B GLY* 4.2 4.9 - - - -
403B LEU* 3.8 11.1 - - - +
407B LEU* 1.4 73.5 - - - +
409B LEU* 1.4 59.3 + - - +
410B LEU* 4.1 0.4 - - - -
428B ILE* 3.1 18.2 - - - +
430B ALA 2.9 28.7 + - - -
431B GLY 3.8 0.7 - - - -
432B ASN 2.9 9.8 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.5 37.2 - - + +
398B ILE* 3.8 15.7 - - + -
407B LEU* 3.7 0.4 - - - +
408B SER* 1.4 80.2 + - - +
410B LEU* 1.4 59.7 - - - +
411B ILE* 4.2 26.7 - - + -
422B PHE* 5.1 6.1 - - + -
425B LEU* 4.7 7.2 - - + -
428B ILE* 4.1 23.3 - - + -
432B ASN 3.5 2.7 + - - +
433B ILE* 3.4 29.0 - - + -
434B TYR* 2.7 33.5 + - - +
435B ILE* 5.8 0.2 - - - -
449B TRP* 4.5 11.2 - - + -
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Residues in contact with LEU 410 (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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376B PHE* 4.3 5.4 - - + -
377B LEU 3.0 19.5 + - - +
378B ASN* 3.6 35.4 - - + +
379B ILE* 2.8 29.3 + - - +
380B GLN* 5.2 1.6 - - - +
404B TYR* 3.8 30.5 - - + -
407B LEU* 3.7 39.9 - - + +
408B SER 4.1 1.1 - - - -
409B LEU* 1.4 84.8 - - - +
411B ILE* 1.3 63.4 + - - +
412B LEU* 4.1 14.1 - - + -
434B TYR* 3.3 9.6 - - + +
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.5 21.5 - - + +
389B PHE* 3.7 26.0 - - + -
409B LEU* 4.2 16.8 - - + -
410B LEU* 1.3 77.4 - - - +
412B LEU* 1.3 60.9 + - - +
414B GLN* 4.9 2.7 - - + -
417B ILE* 4.0 10.1 - - + -
420B LEU* 3.9 23.6 - - + -
422B PHE* 4.0 17.0 - - + -
434B TYR 2.9 5.9 + - - +
435B ILE* 3.3 25.8 - - + -
436B THR 3.1 22.7 + - - -
438B ASN* 3.1 19.5 + - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASN* 4.5 0.4 - - - +
379B ILE 3.0 15.5 + - - +
380B GLN* 3.7 38.4 - - + +
410B LEU* 4.4 18.6 - - + -
411B ILE* 1.3 76.8 - - - +
413B LYS* 1.4 82.8 + - + +
414B GLN* 3.0 28.2 + - - +
434B TYR* 4.2 22.9 - - + +
436B THR* 3.1 21.1 - - - +
437B ASP* 5.1 0.9 - - - +
438B ASN* 3.3 1.9 + - - -
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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