Contacts of the helix formed by residues 395 - 404 (chain F) in PDB entry 5UHA
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 THR 395 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860C GLU* 5.4 5.2 - - - +
392F ARG* 3.6 22.4 - - - +
393F GLU 3.7 1.3 + - - +
394F PRO* 1.3 74.2 - - - +
396F PRO* 1.3 75.8 - - - +
397F GLU* 3.7 17.9 + - - +
398F GLU* 3.0 39.2 + - - +
399F LEU* 3.1 12.0 + - - +
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Residues in contact with PRO 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860C GLU* 4.2 27.8 - - + +
394F PRO 3.7 2.4 - - - +
395F THR* 1.3 86.5 - - - +
397F GLU* 1.3 70.2 + - + +
399F LEU* 3.2 9.3 + - + +
400F ALA* 3.1 24.5 + - - +
407F PRO* 5.3 4.3 - - + +
410F VAL* 4.5 11.4 - - + +
411F LEU* 3.6 33.0 - - + -
414F GLN* 5.9 4.7 - - - +
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Residues in contact with GLU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLU* 5.4 2.9 - - - +
395F THR* 3.2 15.4 + - - +
396F PRO* 1.3 82.8 - - + +
398F GLU* 1.3 61.7 + - - +
400F ALA* 3.8 1.6 - - - +
401F LYS* 3.2 32.2 + - + +
407F PRO* 4.7 17.4 - - + +
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Residues in contact with GLU 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F LEU* 4.5 7.9 - - + +
390F LEU* 3.3 21.4 - - - +
392F ARG* 2.6 33.5 + - - -
394F PRO* 3.5 8.9 - - + +
395F THR* 3.0 37.3 + - - +
397F GLU* 1.3 79.4 - - + +
399F LEU* 1.3 64.5 + - - +
400F ALA 3.3 0.3 + - - -
401F LYS* 3.5 14.2 + - - +
402F GLU* 3.7 9.9 + - - +
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Residues in contact with LEU 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F LEU* 4.1 24.9 - - + -
382F ILE* 4.0 8.5 - - + +
383F GLN* 3.6 42.2 - - + +
386F LEU* 3.7 20.6 - - + -
394F PRO* 3.6 28.5 - - + +
395F THR 3.1 9.3 + - - +
396F PRO* 3.7 8.7 - - + +
398F GLU* 1.3 75.5 - - - +
400F ALA* 1.3 65.9 + - - +
402F GLU* 3.3 12.1 + - - +
403F MET* 3.6 15.3 + - - +
410F VAL* 4.6 5.8 - - + -
414F GLN* 4.4 16.6 - - - +
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Residues in contact with ALA 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F PRO 3.1 12.0 + - - +
397F GLU 3.8 5.4 - - - +
398F GLU 3.3 0.2 - - - -
399F LEU* 1.3 76.2 - - - +
401F LYS* 1.3 59.3 + - + +
402F GLU 3.1 0.7 + - - -
403F MET* 3.1 1.7 + - - -
404F ASP* 2.8 18.9 + - - +
405F ILE* 2.7 25.0 + - - -
406F THR 3.3 26.7 - - - +
407F PRO* 3.4 20.4 - - + -
410F VAL* 3.5 11.6 - - + +
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Residues in contact with LYS 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397F GLU* 3.2 23.1 - - + +
398F GLU* 3.5 7.6 + - - +
399F LEU 3.4 0.6 - - - -
400F ALA* 1.3 76.2 - - + +
402F GLU* 1.3 63.6 + - - +
403F MET 3.5 0.2 + - - -
405F ILE* 3.6 42.4 + - + +
407F PRO* 6.1 2.0 - - + -
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Residues in contact with GLU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F ILE* 3.7 33.2 - - + +
385F GLU* 3.8 19.2 - - - +
386F LEU* 3.7 23.7 - - + +
398F GLU 3.7 7.8 + - - +
399F LEU 3.3 10.5 + - - +
400F ALA 3.1 1.2 + - - -
401F LYS* 1.3 82.2 - - - +
403F MET* 1.3 60.8 + - - +
405F ILE* 5.6 0.7 - - - +
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Residues in contact with MET 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375F VAL* 4.4 15.3 - - + +
378F LYS* 4.1 27.4 - - + +
379F LEU* 3.7 39.5 - - + +
382F ILE* 4.6 17.9 - - + -
399F LEU 3.8 13.9 - - - +
400F ALA* 3.1 2.2 + - - +
401F LYS 4.7 0.2 - - - -
402F GLU* 1.3 80.6 - - + +
404F ASP* 1.3 79.3 + - + +
405F ILE* 3.7 3.8 - - - +
410F VAL* 5.4 3.1 - - + -
413F ILE* 5.9 3.6 - - + -
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Residues in contact with ASP 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F ALA* 2.8 32.5 + - - +
403F MET* 1.3 87.4 - - + +
405F ILE* 1.3 70.2 + - - +
406F THR* 2.9 53.3 + - - +
409F LYS* 4.0 13.7 - - - +
410F VAL* 3.7 7.7 - - - +
413F ILE* 5.3 3.5 - - - +
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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