Contacts of the strand formed by residues 407 - 411 (chain C) in PDB entry 3A4S
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 407 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG 2.9 14.0 + - - +
18B LYS 4.1 6.1 - - - -
19B ASP* 3.7 8.3 - - - +
20B HIS* 3.4 45.4 - - + +
344C ARG* 3.2 41.5 - - + +
346C GLN* 3.4 48.0 - - + +
385C PHE 4.4 0.7 - - - +
386C PHE* 3.0 25.6 - - - -
406C ASP* 1.3 74.0 - - - +
408C ILE* 1.3 64.0 + - - +
409C GLU* 4.0 2.8 + - + +
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Residues in contact with ILE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C LEU* 4.8 24.0 - - + -
344C ARG 2.8 19.3 + - - +
345C VAL* 3.0 19.9 - - + +
346C GLN* 2.8 25.1 + - - -
364C LEU* 5.6 2.0 - - + -
367C LEU* 4.8 7.6 - - + -
384C PHE* 3.9 27.4 - - + -
385C PHE 3.6 11.0 - - - +
386C PHE* 3.8 24.2 - - + -
391C LEU* 4.2 18.4 - - + -
400C LEU* 6.3 0.2 - - + -
402C LEU* 5.0 9.2 - - + -
406C ASP* 5.1 2.9 - - + +
407C LEU* 1.3 84.1 - - - +
409C GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS* 3.5 19.3 - - + +
21B PRO 3.3 5.2 - - - +
22B PHE* 3.0 19.1 - - + -
23B GLY* 3.3 12.6 + - - -
24B PHE 4.2 6.3 - - - +
25B VAL* 5.2 3.6 - - - +
346C GLN* 2.7 42.9 + - + +
384C PHE* 3.5 3.1 - - - +
385C PHE* 2.8 40.0 + - + +
407C LEU* 4.0 3.5 + - + +
408C ILE* 1.3 74.8 - - - +
410C VAL* 1.3 59.9 + - - +
411C TRP* 3.3 30.5 - - + -
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.4 17.2 - - - -
345C VAL* 3.7 11.4 - - + -
346C GLN 2.9 16.8 + - - +
347C GLY* 3.7 9.2 - - - -
348C LYS* 4.5 1.4 + - - +
352C GLN* 5.9 0.7 - - - +
371C TYR* 3.3 37.9 - - + +
382C LEU* 4.2 14.4 - - + -
383C SER 4.0 2.5 - - - +
384C PHE* 3.7 36.6 - - + -
409C GLU* 1.3 75.1 - - - +
411C TRP* 1.3 71.5 + - - +
412C GLY* 3.7 5.9 + - - +
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Residues in contact with TRP 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 3.6 30.6 - + - -
23B GLY* 4.7 8.3 - - - -
25B VAL* 6.4 1.1 - - + -
348C LYS* 6.0 5.1 - - + +
381C LYS 3.8 5.0 - - - +
382C LEU* 3.8 1.7 - - - -
383C SER* 3.1 40.9 + - - +
385C PHE* 3.4 35.6 - + + -
409C GLU* 3.3 44.6 - - + -
410C VAL* 1.3 78.5 - - - +
412C GLY* 1.3 69.9 + - - +
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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
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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