Contacts of the strand formed by residues 341 - 346 (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 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C GLN 3.6 2.1 + - - +
340C GLU* 1.3 69.2 - - - +
342C ARG* 1.3 58.8 - - - +
343C LEU* 3.3 16.1 + - + +
358C LEU 3.0 37.2 + - - +
359C SER 3.6 2.5 - - - +
360C PRO* 3.3 37.7 - - + -
397C PRO* 4.0 19.1 - - + -
402C LEU* 3.7 35.7 - - + +
403C GLU* 4.0 5.2 - - - +
404C SER* 3.7 23.6 - - - +
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Residues in contact with ARG 342 (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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340C GLU 3.4 7.8 + - - +
341C LEU* 1.3 68.5 - - - +
343C LEU* 1.3 64.8 + - - +
344C ARG* 4.6 3.1 - - - +
355C GLU* 3.6 27.6 + - + +
356C ILE 4.4 0.9 - - - +
357C SER* 3.5 31.9 + - - +
404C SER* 3.6 11.0 - - - -
405C GLY* 3.4 18.1 + - - -
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LEU* 3.3 22.2 + - + +
342C ARG* 1.3 73.2 - - - +
344C ARG* 1.3 72.3 + - - +
355C GLU* 3.5 3.5 - - - +
356C ILE* 2.7 34.6 + - - +
358C LEU* 4.1 19.7 - - + -
364C LEU* 4.9 2.0 - - + -
367C LEU* 4.0 24.9 - - + -
402C LEU* 4.1 21.5 - - + -
403C GLU 3.4 32.8 - - - +
404C SER* 4.4 0.2 - - - -
405C GLY 4.7 0.2 - - - +
406C ASP* 4.2 17.7 - - + +
408C ILE* 4.8 12.1 - - + -
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Residues in contact with ARG 344 (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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18B LYS 3.9 11.1 + - - -
19B ASP* 5.0 6.5 + - - -
342C ARG 4.6 3.4 - - - +
343C LEU* 1.3 84.1 - - - +
345C VAL* 1.3 64.0 + - - +
346C GLN* 4.3 2.2 + - - +
353C MET* 4.9 16.6 - - - +
354C LEU 3.8 7.4 - - - +
355C GLU* 4.2 26.7 - - + +
356C ILE 4.7 0.2 - - - +
405C GLY* 4.0 17.3 + - - +
406C ASP 3.4 12.1 + - - +
407C LEU* 3.2 33.7 - - + +
408C ILE* 2.8 28.5 + - - +
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Residues in contact with VAL 345 (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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344C ARG* 1.3 78.5 - - - +
346C GLN* 1.3 59.7 + - - +
352C GLN 3.8 1.2 - - - +
353C MET* 3.2 8.0 - - - +
354C LEU 3.0 36.0 + - - +
356C ILE* 5.0 2.9 - - + -
367C LEU* 4.0 26.9 - - + -
371C TYR* 3.7 24.7 - - + -
384C PHE* 4.2 6.7 - - + -
407C LEU* 5.1 0.2 - - - -
408C ILE* 3.0 31.4 - - + +
410C VAL* 3.7 29.8 - - + -
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Residues in contact with GLN 346 (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 19.4 + - - +
22B PHE* 3.5 18.3 + - + +
344C ARG* 5.0 1.7 + - - -
345C VAL* 1.3 74.0 - - - +
347C GLY* 1.3 58.8 + - - +
353C MET* 3.3 35.1 - - + +
407C LEU* 3.4 33.5 - - + +
408C ILE 2.8 6.9 + - - -
409C GLU* 2.7 41.3 + - + +
410C VAL* 2.9 27.2 + - - -
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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