Contacts of the strand formed by residues 407 - 412 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350H LYS* 3.2 28.9 + - - +
351H GLY* 3.3 18.4 - - - -
352H PHE* 3.8 8.3 - - - -
363H GLY 5.0 0.7 + - - -
374H PHE* 3.3 39.4 - - - -
405H GLY 4.5 0.7 + - - -
406H TYR* 1.3 78.0 - - - +
408H GLY* 1.3 57.9 + - - +
423H TRP* 3.2 24.9 - - - -
424H VAL* 4.2 2.5 - - - -
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Residues in contact with GLY 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H SER* 4.8 1.1 - - - -
279H SER* 3.4 14.1 - - - -
350H LYS* 4.3 1.8 - - - -
352H PHE* 3.8 9.3 - - - -
407H SER* 1.3 75.6 - - - +
409H SER* 1.3 60.2 + - - -
422H PHE* 3.5 5.2 - - - +
423H TRP* 3.1 50.5 + - - +
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Residues in contact with SER 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H ILE 4.5 0.3 - - - +
228H SER* 4.8 6.4 - - - -
229H GLU* 3.8 13.4 + - - +
279H SER* 3.7 21.7 + - - -
280H CYS 3.8 15.8 + - - -
281H TYR* 4.6 5.8 - - - +
352H PHE* 3.9 14.1 - - - +
353H SER 5.6 0.2 - - - -
354H PHE* 3.6 28.5 - - - -
408H GLY* 1.3 75.1 - - - -
410H PHE* 1.3 67.2 + - - +
421H CYS 3.8 4.9 - - - -
422H PHE* 4.3 1.3 - - - +
423H TRP* 3.9 6.3 + - - -
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Residues in contact with PHE 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H TYR* 4.3 13.9 - + - -
122H ILE* 3.3 53.6 - - + +
123H SER* 5.0 0.4 - - - -
124H CYS* 4.1 14.6 - - - -
229H GLU* 2.9 11.9 - - - +
354H PHE* 4.8 0.8 - - - -
409H SER* 1.3 78.9 - - - +
411H VAL* 1.3 72.6 + - - +
412H GLN* 4.5 2.7 - - - -
421H CYS* 3.0 60.7 + - + +
422H PHE* 3.4 36.1 - - - -
423H TRP* 3.9 10.3 - + + -
445H SER* 3.9 8.5 - - - -
446H PHE 4.2 1.3 - - - -
447H CYS* 4.1 7.0 - - - -
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Residues in contact with VAL 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H LEU* 5.8 0.4 - - + -
124H CYS* 3.6 29.6 + - - +
229H GLU* 3.1 16.6 + - - +
281H TYR* 4.1 13.7 - - + -
282H PRO* 3.7 25.8 - - + -
354H PHE* 5.5 4.5 - - + -
410H PHE* 1.3 78.8 - - - +
412H GLN* 1.3 117.7 + - - +
418H ILE* 3.2 24.9 - - + -
419H ARG 3.7 5.4 - - - +
420H PRO* 5.5 1.3 - - + -
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Residues in contact with GLN 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ILE* 5.1 9.8 - - - +
211E ILE 5.7 0.4 - - - +
100H TYR* 4.2 19.6 + - - -
124H CYS* 4.8 2.9 - - - -
129H CYS* 5.3 0.2 - - - -
410H PHE* 4.5 5.3 - - + -
411H VAL* 1.3 84.4 - - - +
412H HIS* 1.2 73.9 + - - +
413H THR* 3.6 19.0 + - - +
417H CYS 4.3 0.2 - - - +
418H ILE* 3.5 1.4 - - - -
419H ARG* 2.4 79.7 + - + +
421H CYS* 2.9 10.2 - - - -
447H CYS* 2.6 31.7 - - - -
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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