Contacts of the strand formed by residues 406 - 413 (chain A) in PDB entry 5HG1
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LEU* 4.9 8.3 - - + +
397A ILE* 5.6 4.0 - - + -
398A LYS* 4.2 32.0 - - + +
401A LYS* 5.6 5.6 - - + -
403A GLU* 4.5 8.2 + - - -
404A GLU 4.3 0.6 - - - -
405A ARG* 1.3 71.6 - - - +
407A ARG* 1.3 59.8 + - - +
408A SER* 4.0 8.7 - - - -
437A GLY 3.4 9.2 + - - +
438A CYS* 5.2 4.5 - - + -
439A ASP* 2.8 31.4 + - - +
440A VAL* 5.5 2.1 - - + +
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASP* 3.6 9.7 + - - -
223A ASN* 2.9 57.0 + - - +
225A GLU* 5.4 0.3 - - - +
401A LYS* 5.4 11.4 - - - +
403A GLU* 5.8 0.2 - - - +
405A ARG 3.4 4.7 + - - +
406A LEU* 1.3 72.3 - - - +
408A SER* 1.3 71.5 + - - +
409A THR* 2.7 26.3 + - - -
439A ASP* 3.4 27.6 - - + +
440A VAL* 5.8 0.4 - - - +
441A ARG* 3.0 45.2 - - - +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 3.8 6.7 + - - -
225A GLU* 4.0 24.0 + - - +
226A ILE* 4.3 6.1 - - - +
394A LEU* 4.3 23.3 - - - +
397A ILE* 4.7 7.2 - - - +
401A LYS* 6.3 0.9 - - - -
406A LEU* 4.0 8.9 - - - -
407A ARG* 1.3 80.2 + - - +
409A THR* 1.3 68.4 + - - +
410A ILE* 5.4 0.2 - - - -
439A ASP 3.3 6.4 + - - -
440A VAL* 3.4 11.3 - - - +
441A ARG 3.2 21.8 + - - -
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASP* 2.7 31.7 + - - +
223A ASN* 3.2 13.9 + - - +
224A CYS* 3.0 37.7 - - + -
225A GLU 3.4 5.0 + - - -
226A ILE 3.8 2.8 + - - -
407A ARG* 2.7 23.6 + - - -
408A SER* 1.3 75.4 + - - +
410A ILE* 1.3 66.2 + - - +
441A ARG* 3.3 15.2 - - + +
443A LEU* 3.9 24.7 - - + -
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Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A CYS* 4.3 0.2 - - - -
226A ILE* 3.5 39.3 - - + +
228A LEU* 4.0 16.4 - - + -
390A LEU* 4.2 17.0 - - + -
394A LEU* 4.2 10.8 - - + -
409A THR* 1.3 74.2 - - - +
411A GLY* 1.3 67.3 + - - +
412A VAL* 3.8 18.6 - - + +
431A VAL* 5.8 0.2 - - + -
440A VAL* 3.9 18.8 - - + -
441A ARG 3.0 6.4 + - - +
442A PHE* 3.4 30.9 - - + -
443A LEU* 2.8 27.2 + - - +
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Residues in contact with GLY 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.5 9.2 - - - +
217A CYS* 3.2 31.9 - - - -
224A CYS* 3.5 7.2 - - - -
226A ILE 2.9 13.6 + - - +
227A GLY* 3.4 4.2 - - - -
228A LEU* 2.7 33.1 + - - +
410A ILE* 1.3 71.4 - - - +
412A VAL* 1.4 53.5 + - - -
443A LEU 3.7 0.7 - - - -
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.9 2.8 - - - +
217A CYS* 4.1 0.4 - - - -
228A LEU* 3.2 25.8 - - + +
230A VAL 5.3 0.7 - - - +
410A ILE* 3.8 23.3 - - + +
411A GLY* 1.4 77.5 - - - +
413A ASP* 1.3 78.4 + - - +
417A TYR* 3.2 52.0 - - + +
442A PHE* 4.0 11.7 - - + -
443A LEU 2.7 19.2 + - - +
444A ARG* 3.4 22.5 - - - +
445A SER 3.4 5.4 + - - -
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.8 19.4 + - + +
228A LEU 2.9 8.4 + - - +
229A ILE* 3.5 10.6 - - + +
230A VAL 3.0 24.0 + - - +
412A VAL* 1.3 84.0 - - - +
414A GLY* 1.3 83.7 + - - +
417A TYR* 3.9 3.8 - - - +
418A LYS* 3.3 21.7 + - - +
445A SER* 3.7 12.9 - - - +
446A GLU 5.3 0.2 - - - +
447A ASP 4.7 0.5 - - - -
448A GLY* 3.3 29.5 - - - -
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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