Contacts of the strand formed by residues 409 - 417 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B PRO* 5.5 2.4 - - - +
323B PHE* 3.4 23.6 - - - -
325B VAL* 3.8 26.4 - - + +
408B ALA* 1.3 74.2 - - - +
410B TYR* 1.3 68.8 + - - +
411B VAL* 4.6 4.9 - - + -
430B CYS* 3.0 8.7 - - - +
431B VAL 2.9 37.8 + - - -
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B LEU* 4.1 12.1 - - + -
399B THR 4.7 0.2 - - - -
400B ARG* 3.2 55.3 - - + +
401B GLY 3.7 0.2 + - - -
404B CYS* 3.0 48.1 + - + +
405B PRO 3.2 5.6 + - - -
406B TYR* 4.5 3.3 - - - -
408B ALA* 3.0 37.9 - - + -
409B THR* 1.3 78.0 - - - +
411B VAL* 1.3 64.3 + - - +
412B ASP* 5.3 2.1 - - - +
427B ASP* 3.1 41.5 - - + +
429B PHE 3.4 4.9 - - - +
430B CYS* 3.8 9.6 - - + -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 3.9 28.0 - - + -
327B GLY 4.7 5.6 - - - +
339B PHE* 3.9 17.7 - - + -
409B THR* 4.6 8.3 - - + -
410B TYR* 1.3 79.5 - - - +
412B ASP* 1.3 74.2 + - - +
427B ASP* 3.2 2.0 - - - -
428B ALA 2.8 31.7 + - - -
429B PHE* 2.8 34.5 + - + +
431B VAL* 5.4 3.6 - - + -
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B TYR 5.3 2.4 - - - +
411B VAL* 1.3 91.8 - - - +
413B TRP* 1.3 63.0 + - - +
414B HIS* 4.3 6.9 + - + -
424B THR* 3.7 16.8 - - + -
425B ILE 3.4 4.0 - - - +
426B ARG* 3.0 34.9 - - - +
427B ASP* 3.1 6.8 + - - +
428B ALA* 4.4 0.4 - - - -
429B PHE* 4.0 5.4 - - - -
1747B CU 4.3 12.1 - - - -
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Residues in contact with TRP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 3.5 29.6 + - + +
100B GLU* 5.2 3.6 - - + -
341B LEU* 3.5 36.0 - - + +
343B ALA* 3.8 15.9 - - + -
392B GLY* 3.0 36.8 - - - -
393B LYS* 3.7 7.9 - - - -
412B ASP* 1.3 76.4 - - - +
414B HIS* 1.3 72.6 + - - +
415B PHE* 3.8 27.9 + + + -
417B LEU* 4.4 2.5 - - + -
424B THR* 3.4 2.1 - - - +
425B ILE* 2.8 60.7 + - + +
428B ALA* 3.5 19.5 - - + -
429B PHE* 4.1 15.7 - + + -
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Residues in contact with HIS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 5.5 1.6 - - - +
63B LEU 4.2 11.0 + - - +
64B SER* 4.8 5.2 - - - -
65B ARG* 4.1 42.5 - - + +
68B LEU* 4.0 20.5 - - + +
412B ASP* 4.5 6.4 - - + +
413B TRP* 1.3 87.7 + - - +
415B PHE* 1.3 60.7 + - - +
422B PRO* 5.5 0.7 - - + -
423B LYS 3.3 7.2 - - - +
424B THR* 3.1 35.1 + - + +
1747B CU 2.2 31.1 - - - -
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Residues in contact with PHE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.9 6.5 - - - +
99B VAL 5.6 0.2 - - - -
393B LYS* 5.8 5.4 - - + -
413B TRP* 3.8 33.4 - + + -
414B HIS* 1.3 75.4 - - - +
416B LEU* 1.3 62.7 + - - +
417B LEU* 3.7 39.7 - - + -
419B SER* 5.9 1.6 - - - -
421B ALA 4.7 0.2 - - - +
422B PRO* 3.5 3.1 - - - +
423B LYS* 2.8 78.6 + - + -
424B THR 4.1 2.9 - - - -
425B ILE* 3.6 28.7 - - + -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.5 41.5 - - + +
72B MET* 4.0 20.2 - - + -
98B SER* 3.4 2.1 - - - -
99B VAL* 3.0 57.4 + - + +
415B PHE* 1.3 75.4 - - - +
417B LEU* 1.3 62.5 + - - +
419B SER* 4.2 7.0 - - - +
420B GLN* 3.7 11.4 - - - +
421B ALA 3.5 41.7 - - - +
422B PRO* 3.6 3.4 - - + -
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE 3.3 6.1 - - - +
98B SER* 3.6 20.4 - - - -
99B VAL 4.4 7.0 - - - +
100B GLU* 5.2 1.6 - - + -
343B ALA* 3.9 25.6 - - + -
344B PHE* 5.1 1.8 - - + -
393B LYS* 3.5 53.8 - - + -
413B TRP* 4.4 1.6 - - + -
415B PHE* 3.7 39.6 - - + -
416B LEU* 1.3 88.7 - - - +
418B GLU* 1.3 76.1 + - - +
419B SER* 3.4 6.4 + - - -
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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