Contacts of the strand formed by residues 302 - 306 (chain A) in PDB entry 5FS9
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A VAL* 3.6 1.4 - - - +
301A LYS* 1.3 83.0 - - - +
303A ILE* 1.3 66.8 + - - +
329A GLU* 2.7 36.0 + - - +
331A ILE* 4.2 4.0 - - - +
378A LYS* 4.5 5.8 - - - -
390A GLU 4.7 0.9 - - - -
391A THR* 2.8 26.6 + - - -
392A ASP* 2.8 39.5 + - - +
393A HIS 3.5 1.7 + - - -
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 4.2 5.4 - - + -
296A ILE* 3.9 16.4 - - + -
297A SER* 3.8 30.5 - - - +
300A VAL* 3.7 11.4 - - + -
301A LYS 5.8 0.2 - - - -
302A SER* 1.3 79.2 + - - +
304A THR* 1.3 68.5 + - - +
305A ILE 4.1 0.2 - - - -
319A LEU* 4.0 37.0 - - + -
329A GLU 3.0 9.7 + - - +
330A VAL* 3.4 8.2 - - + +
331A ILE* 2.9 25.8 + - - +
391A THR* 3.6 0.2 - - - -
393A HIS* 3.7 12.6 - - + +
395A VAL* 4.0 21.1 - - + -
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 1.3 74.1 - - - +
305A ILE* 1.3 65.5 + - - +
306A ILE* 3.9 4.7 + - + -
331A ILE* 3.3 24.8 - - + +
333A LEU* 3.7 29.4 - - + -
381A ILE* 3.9 12.8 - - + -
389A VAL* 3.8 1.8 - - + +
391A THR* 2.9 33.1 + - - +
393A HIS 3.0 8.2 + - - -
394A ILE* 3.3 5.7 - - - +
395A VAL 2.8 30.7 + - - +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 5.0 0.2 - - + -
304A THR* 1.3 77.3 - - - +
306A ILE* 1.3 65.5 + - - +
307A GLY 4.1 7.6 - - - +
312A GLY* 3.8 27.8 - - - +
315A LEU* 3.7 11.4 - - + -
316A ALA* 3.2 43.1 - - + +
319A LEU* 3.8 22.7 - - + -
330A VAL* 4.0 11.9 - - + -
331A ILE 2.7 11.9 + - - +
332A GLN* 3.3 5.5 - - + +
333A LEU* 2.9 27.7 + - - +
395A VAL* 3.3 19.1 - - + +
397A ALA* 4.8 3.6 - - + -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.0 24.7 - - + -
270A ILE* 4.2 16.8 - - + -
304A THR* 4.4 4.5 - - + -
305A ILE* 1.3 75.2 - - - +
307A GLY* 1.3 61.2 + - - +
333A LEU* 3.5 28.9 - - + +
334A PHE* 5.6 1.8 - - - -
335A PRO* 6.2 1.6 - - + -
369A VAL* 4.4 12.6 - - + -
372A VAL* 6.0 0.9 - - + -
381A ILE* 4.8 7.6 - - + -
394A ILE* 3.7 32.1 - - + -
395A VAL 2.8 11.0 + - - +
396A ALA* 4.7 4.3 - - + -
397A ALA* 2.8 30.3 + - - +
398A VAL* 3.5 14.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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