Contacts of the strand formed by residues 407 - 415 (chain C) in PDB entry 2R7D
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 TRP 407 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C PHE* 3.7 11.0 - + - -
399C ILE* 4.8 10.9 - - + +
402C GLN* 4.3 15.1 + - + -
405C ARG* 3.4 74.7 + - + +
406C VAL* 1.3 74.5 - - - +
408C ASP* 1.3 62.7 + - - +
409C ALA 3.5 1.2 + - - -
423C ILE* 3.9 25.8 - - + -
425C ASP* 4.5 11.0 - - + -
426C LEU* 3.6 45.8 - - + -
443C GLN* 3.3 9.0 + - - -
444C VAL* 2.7 49.8 + - + +
445C GLN* 4.8 0.4 - - - -
446C PHE* 3.6 29.5 - + + +
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Residues in contact with ASP 408 (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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406C VAL 5.3 2.2 - - - +
407C TRP* 1.3 71.3 - - - +
409C ALA* 1.3 61.1 + - - +
410C VAL* 5.5 0.4 - - - -
423C ILE* 3.7 10.9 - - - +
424C PRO* 3.3 21.8 - - + +
425C ASP* 5.2 9.4 - - - +
442C LEU 3.7 4.1 - - - +
443C GLN* 3.4 23.7 + - - +
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Residues in contact with ALA 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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407C TRP 3.5 1.0 + - - +
408C ASP* 1.3 73.8 - - - +
410C VAL* 1.3 71.7 + - - +
421C LEU* 4.1 12.8 - - + -
422C LEU 3.1 11.4 - - - +
423C ILE* 3.6 21.3 - - + -
441C ALA* 3.4 4.3 - - - +
442C LEU* 2.9 32.4 + - + +
444C VAL* 4.0 22.0 - - + -
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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
----------------------------------------------------------
305C LEU* 4.0 33.7 - - + -
306C PRO* 4.9 1.6 - - + -
408C ASP 5.5 0.4 - - - -
409C ALA* 1.3 82.6 - - - +
411C VAL* 1.3 78.1 + - - +
412C VAL* 3.4 7.1 + - + +
421C LEU* 3.4 2.6 - - - -
422C LEU* 2.7 39.3 + - + +
424C PRO* 4.6 8.3 - - + -
439C GLY* 4.1 15.7 - - - +
440C THR 3.5 9.0 - - - +
441C ALA* 4.8 8.5 - - + -
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Residues in contact with VAL 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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306C PRO* 4.2 1.4 - - - +
410C VAL* 1.3 76.7 - - - +
412C VAL* 1.3 62.1 + - - +
413C ASP 3.8 18.6 - - - +
414C ARG* 4.3 2.2 - - + -
419C ALA* 4.3 8.3 - - + -
420C THR 3.7 5.6 - - - +
421C LEU* 4.3 16.8 - - + +
434C THR* 4.8 0.7 - - + -
436C ALA* 4.1 18.8 - - + +
437C ALA 3.7 26.7 - - - +
438C PRO* 3.6 9.0 - - + +
439C GLY* 2.8 26.3 + - - -
440C THR 3.0 16.3 + - - +
442C LEU* 3.8 18.2 - - + -
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Residues in contact with VAL 412 (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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305C LEU* 4.0 28.3 - - + -
306C PRO* 4.0 23.5 - - + +
309C TRP* 3.4 50.2 - - + +
310C ALA* 5.2 1.6 + - - +
410C VAL* 3.8 10.8 - - + +
411C VAL* 1.3 77.8 - - - +
413C ASP* 1.3 65.1 + - - +
420C THR* 3.1 24.1 + - - +
421C LEU 5.0 0.2 - - - -
422C LEU* 4.0 20.2 - - + -
429C ASP* 5.7 0.2 - - + -
438C PRO* 4.8 3.6 - - - +
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Residues in contact with ASP 413 (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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309C TRP* 4.2 11.5 + - + +
313C LYS* 3.5 26.6 + - - +
411C VAL* 3.7 5.9 - - - +
412C VAL* 1.3 83.1 - - - +
414C ARG* 1.3 95.1 + - - +
415C ARG* 5.4 1.6 - - - +
419C ALA* 3.4 1.0 - - - -
420C THR* 2.9 44.6 + - - +
438C PRO* 4.7 6.7 - - - +
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Residues in contact with ARG 414 (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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411C VAL* 4.3 4.9 - - + -
413C ASP* 1.3 98.3 + - - +
415C ARG* 1.3 59.9 + - - +
416C GLY 2.7 28.2 + - - +
417C ALA* 3.6 16.8 + - - +
418C GLN 3.1 10.0 + - - +
419C ALA* 3.9 4.9 - - + +
420C THR* 4.7 1.8 - - - +
434C THR 2.5 27.0 + - - -
435C PRO* 3.1 17.4 + - - +
436C ALA 2.7 27.6 + - - +
437C ALA* 4.0 12.8 - - - +
438C PRO* 4.0 12.3 - - + +
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Residues in contact with ARG 415 (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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413C ASP* 5.4 1.8 - - - +
414C ARG* 1.3 76.0 - - - +
416C GLY* 1.3 60.1 + - - +
417C ALA 3.2 0.7 + - - -
418C GLN* 2.6 50.9 + - + +
420C THR* 6.1 3.1 - - + -
431C GLN* 5.3 7.9 + - - +
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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