Contacts of the strand formed by residues 251 - 255 (chain H) in PDB entry 5FHX
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 251 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249H GLY 4.1 0.4 + - - -
250H PRO* 1.3 73.1 - - - +
252H VAL* 1.3 60.3 + - - +
253H PHE* 3.7 32.9 + - - -
272H LEU 3.3 2.8 - - - +
274H LYS* 3.0 34.0 + - - +
275H ASP* 4.5 4.0 + - - +
246L GLU* 5.6 0.2 + - - -
250L SER* 5.4 0.9 + - - -
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Residues in contact with VAL 252 (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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250H PRO* 4.1 5.3 + - + +
251H SER* 1.3 73.4 + - - +
253H PHE* 1.3 62.7 + - - +
271H CYS* 3.8 35.4 - - + -
272H LEU 3.4 3.8 - - - +
273H VAL* 4.1 13.2 - - + -
327H CYS* 4.4 0.7 - - - -
329H VAL* 3.8 39.5 - - + -
338H VAL* 4.3 20.0 - - + +
340H LYS* 4.0 23.7 - - + +
246L GLU* 3.2 15.8 - - - +
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Residues in contact with PHE 253 (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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251H SER* 3.7 37.9 - - - -
252H VAL* 1.3 75.6 - - - +
254H PRO* 1.3 67.4 - - - +
271H CYS* 3.3 6.2 - - - +
272H LEU* 2.8 61.7 + - + +
274H LYS* 4.4 13.9 - - + -
275H ASP* 5.5 1.3 - - - -
340H LYS* 5.0 0.7 - - - -
244L SER* 3.4 12.3 - - - +
246L GLU* 3.3 25.6 - - + -
247L GLN* 3.5 58.6 - - + +
250L SER* 4.2 11.9 - - - -
252L THR* 5.7 1.1 - - + -
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Residues in contact with PRO 254 (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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253H PHE* 1.3 86.0 - - + +
255H LEU* 1.3 64.0 + - - +
256H ALA* 3.4 10.6 + - + +
270H GLY 3.9 4.7 - - - +
271H CYS* 4.8 1.1 - - - -
340H LYS* 4.3 16.5 - - + -
341H LYS 4.6 8.5 - - - +
342H VAL* 4.4 23.3 - - + -
242L PRO 5.0 3.3 - - - +
244L SER* 3.5 34.4 + - - +
246L GLU* 4.3 13.2 - - + +
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Residues in contact with LEU 255 (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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254H PRO* 1.3 74.5 - - - +
256H ALA* 1.4 63.9 + - - +
269H LEU* 3.3 6.1 - - - -
270H GLY* 2.8 44.9 + - - +
271H CYS 3.6 26.9 - - - +
272H LEU* 4.0 15.7 - - + +
310H SER* 3.8 21.1 - - - +
311H SER 4.3 1.8 - - - +
312H VAL* 4.4 9.0 - - + -
342H VAL* 3.4 3.5 - - - +
241L PHE* 3.6 36.9 - - + +
242L PRO 5.6 2.7 - - - +
254L SER 5.9 1.6 - - - +
256L VAL* 3.8 26.7 - - + -
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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