Contacts of the strand formed by residues 409 - 417 (chain C) in PDB entry 2C11
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 THR 409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323C PHE* 4.0 15.8 + - - -
325C VAL* 3.8 36.1 - - + +
408C ALA* 1.3 72.4 - - - +
410C TYR* 1.3 68.2 + - - +
411C VAL* 4.0 5.3 + - + +
430C CYS* 3.3 3.5 - - - -
431C VAL* 2.7 40.5 + - + +
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Residues in contact with TYR 410 (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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398C LEU* 4.1 14.6 - - + -
400C ARG* 3.0 70.9 - - + +
404C CYS* 3.3 16.4 + - + +
405C PRO 2.7 20.2 + - - -
406C TYR 3.7 10.1 - - - -
408C ALA* 3.4 28.0 + - + -
409C THR* 1.3 77.5 - - - +
411C VAL* 1.3 63.6 + - - +
412C ASP* 4.7 1.7 - - - +
427C ASP* 3.6 30.1 - - + +
429C PHE 3.6 2.5 - - - -
430C CYS* 3.9 18.2 - - + -
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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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325C VAL* 4.3 16.8 - - + -
327C GLY 4.8 6.7 - - - +
339C PHE* 4.0 26.0 - - + -
409C THR* 4.5 9.0 - - + +
410C TYR* 1.3 77.9 - - - +
412C ASP* 1.3 82.6 + - - +
427C ASP* 2.8 3.5 - - - -
428C ALA 2.6 32.9 + - - -
429C PHE* 2.8 30.5 + - + +
431C VAL* 5.1 3.8 - - + -
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Residues in contact with ASP 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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65C ARG* 5.3 2.7 + - - +
410C TYR 4.7 1.4 - - - +
411C VAL* 1.3 93.3 - - - +
413C TRP* 1.3 65.2 + - - +
414C HIS* 4.6 2.8 + - + -
424C THR* 3.7 18.8 - - + +
425C ILE 3.3 5.4 - - - +
426C ARG* 3.3 31.3 - - - +
427C ASP* 3.2 19.4 + - - +
428C ALA* 4.4 1.1 - - - -
429C PHE* 3.8 7.3 - - - -
1744C CU 4.5 11.7 - - - -
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Residues in contact with TRP 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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62C ASP* 2.9 39.2 + - + +
100C GLU* 5.6 5.4 - - + -
341C LEU* 3.3 30.2 + - + +
343C ALA* 4.3 12.1 - - + -
392C GLY* 3.7 30.5 - - - -
393C LYS* 4.2 6.7 - - - -
395C THR* 4.0 14.1 - - + -
412C ASP* 1.3 78.7 - - - +
414C HIS* 1.3 75.6 + - - +
415C PHE* 3.7 43.5 - + + -
417C LEU* 4.6 4.3 - - + -
423C LYS 3.9 0.3 - - - +
424C THR* 3.2 2.4 - - - -
425C ILE* 2.8 36.6 + - + +
428C ALA* 3.8 17.9 - - + -
429C PHE* 3.8 16.4 - + + -
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Residues in contact with HIS 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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62C ASP* 5.4 1.1 - - - +
63C LEU 3.9 18.4 + - - +
64C SER* 3.4 29.9 - - - -
65C ARG* 3.4 42.7 + - + +
68C LEU* 4.1 5.6 - - + +
412C ASP* 4.6 3.5 - - + -
413C TRP* 1.3 92.2 + - - +
415C PHE* 1.3 64.4 + - - +
422C PRO* 5.5 1.1 - - + -
423C LYS 3.4 7.0 - - - +
424C THR* 3.1 36.9 + - + +
1744C CU 2.3 30.6 - - - -
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Residues in contact with PHE 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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68C LEU* 3.8 10.8 - - - +
99C VAL 5.5 0.2 - - - -
393C LYS 6.1 1.3 - - - -
413C TRP* 3.7 37.5 - + + -
414C HIS* 1.3 77.8 - - - +
416C LEU* 1.3 60.8 + - - +
417C LEU* 3.9 28.3 - - + -
421C ALA 4.4 0.9 - - - +
422C PRO* 3.1 2.3 - - - +
423C LYS* 3.0 83.1 + - + +
424C THR 4.0 2.0 - - - -
425C ILE* 3.5 28.3 - - + -
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Residues in contact with LEU 416 (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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68C LEU* 3.5 41.7 - - + +
72C MET* 3.7 44.6 - - + -
96C VAL* 6.0 0.2 - - + -
98C SER* 3.4 3.5 - - - -
99C VAL* 3.0 38.9 + - + +
415C PHE* 1.3 72.7 - - - +
417C LEU* 1.3 62.7 + - - +
419C SER 3.9 9.6 - - - +
420C GLN 3.6 3.6 - - - +
421C ALA 3.1 46.7 - - - +
422C PRO* 3.1 4.0 - - + -
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Residues in contact with LEU 417 (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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97C PHE* 3.7 4.0 - - + +
98C SER* 3.2 28.5 - - - -
99C VAL 5.7 1.1 - - - +
343C ALA* 4.2 15.7 - - + -
344C PHE* 4.2 16.4 - - + -
393C LYS* 3.7 52.9 - - + +
413C TRP* 4.6 2.2 - - + -
415C PHE* 3.7 34.6 + - + -
416C LEU* 1.3 79.3 - - - +
418C GLU* 1.3 59.2 + - - +
419C SER* 2.5 26.3 + - - -
423C LYS* 3.7 10.2 + - - -
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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