Contacts of the strand formed by residues 407 - 412 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LYS* 3.4 11.7 + - - +
351C GLY* 3.2 30.1 + - - -
352C PHE* 3.5 12.8 - - - -
363C GLY 5.0 1.7 + - - -
374C PHE* 3.5 39.3 - - - -
405C GLY 4.8 0.3 + - - -
406C TYR* 1.3 78.4 - - - +
408C GLY* 1.3 58.6 + - - +
423C TRP* 3.2 19.1 - - - -
424C VAL* 4.3 2.2 - - - -
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Residues in contact with GLY 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C SER* 4.9 0.9 - - - -
279C SER* 3.6 10.8 - - - -
350C LYS* 4.7 0.9 - - - -
352C PHE* 3.8 8.3 - - - -
407C SER* 1.3 75.7 - - - +
409C SER* 1.3 61.1 + - - -
422C PHE* 3.2 6.6 - - - +
423C TRP* 3.0 56.2 + - - -
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Residues in contact with SER 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE 4.9 0.2 - - - +
228C SER* 4.8 6.1 + - - -
229C GLU* 3.9 13.6 + - - +
279C SER* 3.5 25.5 + - - -
280C CYS 4.0 9.7 + - - +
281C TYR* 4.5 7.3 - - - +
352C PHE* 3.6 19.3 - - - +
353C SER 5.4 0.7 - - - -
354C PHE* 3.4 27.8 - - - -
408C GLY* 1.3 73.5 - - - -
410C PHE* 1.3 63.7 + - - +
411C VAL* 5.6 0.4 - - - -
421C CYS 3.6 4.9 - - - -
423C TRP* 4.4 3.8 + - - -
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C TYR* 4.3 11.9 - + - -
122C ILE* 3.1 68.0 - - + +
124C CYS* 4.1 11.7 - - - -
229C GLU* 3.0 13.9 - - - +
354C PHE* 5.4 0.2 - - - -
409C SER* 1.3 76.2 - - - +
411C VAL* 1.2 70.7 + - - +
412C GLN* 3.8 14.8 - - - -
420C PRO* 4.4 0.4 - - - +
421C CYS* 3.0 59.0 + - + +
422C PHE* 3.6 22.7 - - - -
423C TRP* 3.7 11.4 - + + -
445C SER* 4.0 1.1 - - - -
446C PHE 4.3 2.5 - - - -
447C CYS* 4.3 3.4 - - - -
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Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 5.8 0.9 - - + -
124C CYS* 3.8 14.9 + - - +
229C GLU* 3.0 18.5 + - - +
281C TYR* 3.9 15.7 - - + -
282C PRO* 3.8 24.5 - - + -
354C PHE* 5.4 5.8 - - + -
410C PHE* 1.2 85.8 - - - +
412C GLN* 1.3 110.8 + - - +
418C ILE* 3.0 34.5 - - + -
419C ARG 3.5 6.5 - - - +
420C PRO* 5.6 0.4 - - + -
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Residues in contact with GLN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 5.0 9.7 - - - +
100C TYR* 4.1 18.1 + - - -
124C CYS* 4.5 7.2 - - - -
129C CYS* 4.7 3.0 - - - -
410C PHE* 3.8 11.0 - - + -
411C VAL* 1.3 86.4 - - - +
412C HIS* 1.3 77.9 + - - +
413C THR* 3.7 17.3 + - - +
417C CYS 4.2 1.4 - - - +
418C ILE* 3.8 2.3 - - - -
419C ARG* 2.7 67.8 + - + +
421C CYS* 2.7 14.5 - - - -
447C CYS* 2.7 29.1 - - - -
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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