Contacts of the strand formed by residues 407 - 412 (chain G) in PDB entry 2HU4
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 SER 407 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350G LYS* 3.0 23.4 + - - +
351G GLY* 3.3 25.3 - - - -
352G PHE* 3.5 11.0 - - - -
363G GLY 4.5 1.6 + - - -
374G PHE* 3.6 35.2 - - - -
405G GLY 4.4 0.7 - - - -
406G TYR* 1.3 77.3 - - - +
408G GLY* 1.3 59.1 + - - +
423G TRP* 3.4 20.9 - - - -
424G VAL* 4.4 2.2 - - - -
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Residues in contact with GLY 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G SER* 5.0 0.9 - - - -
279G SER* 3.7 12.1 - - - -
350G LYS* 4.2 0.4 - - - -
352G PHE* 3.8 10.0 - - - -
407G SER* 1.3 77.4 - - - +
409G SER* 1.3 64.0 + - - -
422G PHE* 3.3 5.2 - - - +
423G TRP* 3.0 49.3 + - - -
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Residues in contact with SER 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G SER* 4.8 5.4 - - - -
229G GLU* 4.1 10.8 - - - +
279G SER* 3.8 25.5 + - - -
280G CYS 4.2 10.9 + - - -
281G TYR* 4.4 6.1 - - - +
352G PHE* 3.7 18.3 - - - +
353G SER 5.6 0.4 - - - -
354G PHE* 3.5 29.2 - - - -
408G GLY* 1.3 75.2 - - - -
410G PHE* 1.3 66.1 + - - +
421G CYS 3.6 5.8 - - - -
422G PHE* 4.3 0.7 - - - +
423G TRP* 3.9 6.6 + - - -
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Residues in contact with PHE 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G TYR* 4.5 7.9 - + - -
122G ILE* 3.5 51.1 - - + +
123G SER* 4.8 0.7 - - - -
124G CYS* 4.0 14.1 - - - -
129G CYS* 4.9 1.6 - - - -
229G GLU* 2.9 14.8 - - - +
354G PHE* 4.7 0.9 - - - -
409G SER* 1.3 79.4 - - - +
411G VAL* 1.3 73.9 + - - +
412G GLN* 4.5 5.6 - - - -
420G PRO* 4.2 0.3 - - - +
421G CYS* 2.9 62.6 + - + +
422G PHE* 3.4 36.3 - - - -
423G TRP* 4.1 9.2 - + + -
445G SER* 4.0 14.1 - - - -
447G CYS* 4.2 5.4 - - - -
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Residues in contact with VAL 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 5.6 0.9 - - + -
124G CYS* 3.8 25.3 + - - +
229G GLU* 2.9 14.2 + - - +
281G TYR* 3.9 16.2 - - + -
282G PRO* 3.8 25.4 - - + -
354G PHE* 5.6 1.8 - - + -
410G PHE* 1.3 81.1 - - - +
412G GLN* 1.3 114.2 + - - +
418G ILE* 3.2 33.4 - - + -
419G ARG 3.6 6.1 - - - +
420G PRO* 5.4 2.5 - - + -
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Residues in contact with GLN 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F ILE* 4.4 13.8 - - - +
100G TYR* 3.8 26.1 + - - -
124G CYS* 4.5 9.4 - - - -
129G CYS* 4.7 2.2 - - - -
410G PHE* 4.5 3.6 - - + -
411G VAL* 1.3 87.0 - - - +
412G HIS* 1.3 72.4 + - - +
413G THR* 3.4 20.3 + - - +
417G CYS 4.4 0.5 - - - +
418G ILE* 3.8 1.2 - - - -
419G ARG* 3.1 58.8 + - + +
421G CYS* 3.4 14.3 - - - -
447G CYS* 3.1 24.7 - - - -
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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