Contacts of the strand formed by residues 405 - 409 (chain D) in PDB entry 5HVO
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 VAL 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377D ASP 2.8 13.6 + - - +
378D ALA* 3.1 4.7 - - - +
379D CYS 2.8 26.7 + - - +
395D TYR* 3.6 3.3 - - - -
404D GLY* 1.3 73.3 - - - -
406D LEU* 1.3 65.5 + - - +
407D ILE* 4.4 0.9 - - + -
420D GLY 6.0 0.7 - - - +
422D LEU* 3.5 39.0 - - + -
439D ALA* 3.7 37.0 - - + +
442D MET* 4.0 14.4 - - + -
447D ARG* 3.9 24.5 - - + -
450D LYS* 5.5 3.4 - - + -
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D CYS* 3.9 28.0 - - + +
381D VAL* 4.5 2.2 - - + -
392D SER* 3.8 32.1 - - - -
395D TYR* 4.4 10.1 - - + -
396D ILE* 3.6 28.5 - - + -
404D GLY 3.8 2.4 + - - +
405D VAL* 1.3 75.1 - - - +
407D ILE* 1.3 65.1 + - - +
408D LEU* 4.1 7.4 - - + -
418D LEU* 3.8 11.7 - - + -
420D GLY 5.7 0.8 + - - -
421D SER* 3.4 22.5 - - - +
422D LEU* 2.8 32.4 + - - +
454D LEU* 4.5 12.7 - - + +
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Residues in contact with ILE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D MET* 3.7 29.8 - - + -
378D ALA* 4.7 1.1 - - + -
379D CYS 2.8 12.8 + - - +
380D VAL* 4.2 9.6 - - + -
381D VAL* 2.7 34.8 + - - +
405D VAL* 4.4 2.2 - - + +
406D LEU* 1.3 75.5 - - - +
408D LEU* 1.3 58.1 - - - +
422D LEU* 3.5 26.5 - - + +
424D VAL* 4.1 9.2 - - + -
432D LEU* 4.1 23.8 - - + -
435D ALA* 3.6 28.3 - - + +
436D TYR* 3.7 9.4 - - + -
439D ALA* 3.9 10.1 - - + -
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Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D VAL* 3.5 28.9 - - + -
389D ASN* 5.0 0.9 - - - +
392D SER* 4.2 13.0 - - - +
406D LEU* 4.1 5.8 - - + -
407D ILE* 1.3 75.0 - - - +
409D SER* 1.3 76.5 + - - +
412D ALA* 4.2 11.0 - - + -
414D ALA* 4.0 2.5 - - + -
415D ALA* 3.7 26.0 - - + +
418D LEU* 3.7 31.2 - - + -
421D SER* 3.7 25.8 - - - +
422D LEU 2.9 10.1 + - - +
423D VAL* 3.2 7.0 - - + +
424D VAL* 3.0 24.8 + - - -
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Residues in contact with SER 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D VAL 2.8 19.1 + - - -
382D SER* 3.9 4.0 - - - -
383D SER* 2.7 35.2 + - - -
408D LEU* 1.3 75.5 - - - +
410D GLU* 1.3 58.6 + - - +
411D PHE* 2.9 14.1 + - - +
412D ALA* 3.1 24.1 + - - +
415D ALA* 3.3 13.8 - - - +
424D VAL* 3.4 8.7 - - - -
426D PRO* 3.4 15.6 - - - +
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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