Contacts of the strand formed by residues 409 - 420 (chain C) in PDB entry 2VM8
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 409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.9 15.3 - - + -
35C ILE* 3.6 20.9 - - + -
37C MET* 4.0 14.8 - - - -
42C ILE* 4.0 22.2 - - + -
65C VAL* 3.5 21.8 - - + -
66C ILE 3.5 4.3 - - - -
67C PRO* 5.2 0.2 - - + -
68C GLY* 4.0 1.9 - - - +
400C ARG 5.6 1.1 - - - +
401C ILE* 3.6 25.1 - - + -
406C ASP 4.4 0.7 - - - +
407C ALA* 4.5 1.8 - - - -
408C ASP* 1.3 99.3 - - - +
410C VAL* 1.3 65.1 + - - +
445C VAL 4.1 0.2 - - - +
446C VAL* 3.5 2.0 - - - +
447C ILE* 2.7 54.1 + - + +
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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
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64C MET 3.6 0.3 - - - +
65C VAL* 3.2 5.0 - - - -
66C ILE* 2.7 51.0 + - + +
68C GLY* 4.0 12.8 - - - -
100C GLY* 3.3 32.1 - - - +
409C LEU* 1.3 79.9 - - - +
411C ILE* 1.3 74.5 + - - +
412C TRP* 3.7 24.7 - - + -
443C PRO* 3.8 13.2 - - + -
445C VAL 3.2 11.4 - - - +
446C VAL* 4.0 7.9 - - + -
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Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.7 33.9 - - + -
58C ILE* 3.8 19.7 - - + -
59C GLU 5.3 0.2 - - - +
60C ALA* 4.3 10.5 - - + +
63C ARG* 3.9 21.5 - - + -
64C MET 3.0 8.5 - - - +
65C VAL* 3.7 21.1 - - + -
410C VAL* 1.3 71.2 - - - +
412C TRP* 1.3 54.7 + - - +
444C LEU* 2.7 52.5 + - + +
445C VAL* 2.8 31.8 + - + +
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Residues in contact with TRP 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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63C ARG* 3.9 14.2 - - - +
64C MET* 2.9 48.3 + - + +
66C ILE* 4.4 22.0 - - + -
99C GLY 4.0 6.3 - - - -
100C GLY* 4.7 1.8 - - - -
362C MET* 3.8 27.4 - - + -
363C SER* 3.4 31.6 - - - -
366C TRP* 3.6 28.4 - + + -
380C PHE* 4.1 9.9 - + - -
410C VAL* 3.6 16.1 + - + -
411C ILE* 1.3 75.4 - - - +
413C ASP* 1.3 71.4 + - - +
414C PRO* 3.6 10.5 - - + +
441C GLY* 3.8 8.3 - - - -
442C SER 3.7 14.8 - - - -
443C PRO* 3.4 34.1 - - + -
444C LEU* 4.4 1.7 - - - +
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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
----------------------------------------------------------
63C ARG* 4.6 11.0 + - - +
412C TRP* 1.3 74.7 - - - +
414C PRO* 1.4 64.9 - - - +
415C ASP* 3.3 14.4 + - - +
416C SER* 3.3 30.9 + - - -
441C GLY* 3.0 5.7 + - - -
442C SER* 2.7 48.2 + - - +
444C LEU* 4.0 27.1 - - + +
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Residues in contact with PRO 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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63C ARG* 5.6 5.2 - - + +
64C MET* 3.9 18.2 - - + -
366C TRP* 3.4 47.2 + - + +
412C TRP* 3.6 11.4 - - + +
413C ASP* 1.4 87.2 - - - +
415C ASP* 1.3 78.7 + - - +
440C ARG* 3.1 23.3 + - - +
441C GLY* 4.6 0.2 - - - -
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Residues in contact with ASP 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* 3.3 5.6 - - - +
414C PRO* 1.3 95.9 - - - +
416C SER* 1.3 68.5 + - - +
417C VAL* 3.6 3.8 + - - +
440C ARG* 3.4 35.3 + - - +
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Residues in contact with SER 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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413C ASP* 3.3 29.5 + - - -
415C ASP* 1.3 80.1 - - - +
417C VAL* 1.3 61.9 + - - +
418C LYS* 5.6 5.8 - - - -
439C CYS 4.0 0.3 - - - +
440C ARG* 3.5 2.3 - - - +
441C GLY* 3.2 26.9 + - - -
442C SER* 4.7 9.4 - - - -
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Residues in contact with VAL 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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415C ASP 3.6 3.1 + - - +
416C SER* 1.3 80.4 - - - +
418C LYS* 1.3 73.9 - - - +
438C GLU* 2.9 33.9 - - + +
439C CYS 3.5 11.9 - - - +
440C ARG* 3.9 27.8 - - + -
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Residues in contact with LYS 418 (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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416C SER* 5.6 6.3 - - - -
417C VAL* 1.3 84.3 - - - +
419C THR* 1.3 67.5 + - - +
420C ILE* 6.3 0.2 - - + -
424C THR* 6.5 0.7 - - + -
438C GLU* 3.4 1.7 - - - -
439C CYS* 2.6 43.3 + - + +
442C SER* 3.8 32.7 + - - +
443C PRO* 5.1 4.9 + - - +
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Residues in contact with THR 419 (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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418C LYS* 1.3 85.6 - - - +
420C ILE* 1.3 68.4 + - - +
421C SER* 4.1 7.8 + - - -
424C THR* 5.1 8.1 - - - +
435C GLU* 5.9 0.2 - - - +
436C GLY* 3.6 34.1 - - - +
437C MET 3.1 5.4 - - - +
438C GLU* 3.9 18.4 + - + +
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Residues in contact with ILE 420 (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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360C GLU* 3.7 30.5 - - + +
363C SER* 6.1 0.7 - - - -
364C VAL* 4.0 18.6 - - + -
418C LYS* 6.3 0.4 - - + -
419C THR* 1.3 73.0 - - - +
421C SER* 1.3 64.6 + - - +
424C THR* 6.0 0.7 - - - -
425C HIS* 5.8 1.6 - - + -
432C ASN* 3.4 22.9 - - - +
434C PHE* 3.6 31.0 - - + +
435C GLU* 3.3 2.1 - - - -
436C GLY* 2.7 29.1 + - - -
437C MET* 2.8 24.6 + - + +
439C CYS* 4.2 14.4 - - + -
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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