Contacts of the strand formed by residues 407 - 412 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E LYS* 3.3 18.8 + - - +
351E GLY* 3.3 23.9 + - - -
352E PHE* 3.6 14.7 - - - -
363E GLY 4.9 1.4 + - - -
374E PHE* 3.5 34.7 - - - -
405E GLY 4.7 0.3 + - - -
406E TYR* 1.3 78.8 - - - +
408E GLY* 1.3 59.0 + - - +
423E TRP* 3.3 24.4 - - - -
424E VAL* 4.1 1.8 - - - -
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Residues in contact with GLY 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E SER* 4.8 1.3 - - - -
279E SER* 3.7 11.0 - - - -
350E LYS* 4.2 1.1 - - - -
352E PHE* 3.9 7.4 - - - -
407E SER* 1.3 75.6 - - - +
409E SER* 1.3 61.3 + - - -
422E PHE* 3.3 4.9 - - - +
423E TRP* 2.9 58.4 + - - -
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Residues in contact with SER 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E SER* 4.7 6.3 - - - -
229E GLU* 4.0 12.5 - - - +
279E SER* 3.7 24.7 + - - -
280E CYS 4.1 11.1 + - - +
281E TYR* 4.3 7.6 - - - +
352E PHE* 3.9 18.3 - - - +
353E SER 5.7 0.2 - - - -
354E PHE* 3.5 29.4 - - - -
408E GLY* 1.3 74.3 - - - -
410E PHE* 1.3 63.3 + - - +
421E CYS 3.7 4.3 - - - -
422E PHE* 4.3 1.1 - - - +
423E TRP* 4.3 4.2 + - - -
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Residues in contact with PHE 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E TYR* 4.3 17.7 - + - -
122E ILE* 3.0 62.8 - - + +
123E SER* 4.6 0.4 - - - -
124E CYS* 4.0 16.2 - - - -
229E GLU* 3.1 11.2 - - - +
354E PHE* 4.7 0.6 - - - -
409E SER* 1.3 75.9 - - - +
411E VAL* 1.2 74.8 + - - +
412E GLN* 4.1 4.7 - - - -
420E PRO* 4.2 0.7 - - - +
421E CYS* 3.0 66.6 + - + +
422E PHE* 3.5 30.3 - - - -
423E TRP* 4.0 9.4 - + + -
445E SER* 4.3 1.1 - - - -
446E PHE 4.2 1.1 - - - -
447E CYS* 4.3 0.2 - - - -
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Residues in contact with VAL 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 5.6 0.4 - - + -
124E CYS* 3.9 14.7 + - - +
229E GLU* 2.9 14.6 + - - +
281E TYR* 3.8 16.8 - - + -
282E PRO* 3.5 28.7 - - + -
354E PHE* 5.5 4.0 - - + -
410E PHE* 1.2 87.3 - - - +
412E GLN* 1.3 115.5 - - - +
418E ILE* 3.1 26.7 - - + -
419E ARG 3.5 5.8 - - - +
420E PRO* 5.5 1.1 - - + -
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Residues in contact with GLN 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E TYR* 4.2 16.7 + - - -
124E CYS* 4.5 10.5 - - - -
129E CYS* 4.8 2.3 - - - -
410E PHE* 4.1 7.5 - - + -
411E VAL* 1.3 89.9 - - - +
412E HIS* 1.1 77.6 + - - +
413E THR* 3.8 16.5 + - - +
417E CYS 4.6 0.2 - - - +
418E ILE* 3.7 2.8 - - - -
419E ARG* 2.8 56.9 + - + +
421E CYS* 2.8 15.4 - - - -
447E CYS* 2.6 30.9 - - - -
210G ILE* 5.1 8.6 - - - +
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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