Contacts of the strand formed by residues 441 - 450 (chain C) in PDB entry 2VZE
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 PHE 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C ASP 4.1 1.1 - - - -
393C GLN* 3.8 22.2 - - + -
395C ILE* 3.5 33.7 - - + -
399C GLY 3.8 24.0 - - - -
401C VAL* 3.7 19.1 - - + -
411C GLY* 3.8 9.2 - - - -
412C ILE 3.4 4.9 - - - -
413C ARG* 3.4 64.6 - - + -
414C VAL* 3.9 4.7 - - - -
437C ILE* 3.3 8.0 - - - +
438C ARG 2.9 29.5 + - - +
439C GLY 3.3 0.4 - - - -
440C ASP* 1.3 85.5 - - + +
442C TRP* 1.3 62.4 + - - +
443C LEU* 5.3 0.2 - - - -
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Residues in contact with TRP 442 (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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35C TRP* 3.7 21.1 - + + -
363C GLN* 3.1 22.6 + - - -
365C GLU* 3.7 24.5 - - + -
366C THR* 3.5 22.3 - - + +
411C GLY* 3.0 5.6 - - - -
412C ILE* 2.9 33.3 + - + +
414C VAL* 3.6 25.0 - - + +
422C ILE* 5.4 2.7 - - + -
423C PHE* 3.5 28.7 - + - -
426C TYR* 4.0 7.9 - + - -
433C THR* 3.6 20.4 - - + -
436C ASN* 3.5 47.3 - - + -
437C ILE* 4.0 4.7 - - + +
441C PHE* 1.3 71.4 - - - +
443C LEU* 1.3 69.7 + - - +
444C LEU* 3.9 5.1 - - + +
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Residues in contact with LEU 443 (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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363C GLN* 4.3 0.3 - - - +
395C ILE* 3.1 40.6 - - + -
409C ASP* 4.1 15.5 - - + +
410C ILE 3.7 4.9 - - - +
435C ALA 5.2 3.6 - - - +
436C ASN* 2.7 37.6 + - + +
437C ILE 5.4 0.2 - - - -
438C ARG* 3.2 49.1 - - + +
441C PHE* 4.8 0.4 - - + -
442C TRP* 1.3 88.6 + - - +
444C LEU* 1.3 63.7 + - - +
445C GLY* 3.5 6.4 + - - +
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Residues in contact with LEU 444 (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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361C TYR* 3.2 39.5 - - + +
363C GLN* 2.8 47.0 + - + +
366C THR* 3.6 22.2 - - - +
369C THR* 4.0 5.8 - - + +
410C ILE* 2.9 32.7 + - + +
411C GLY* 3.9 3.4 - - - -
412C ILE* 3.9 26.7 - - + -
436C ASN* 6.0 1.3 - - - -
442C TRP* 3.9 12.3 - - + +
443C LEU* 1.3 73.3 - - - +
445C GLY* 1.3 56.3 + - - +
446C ASP* 3.2 5.6 - - + +
461C ARG* 2.9 11.8 + - - -
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Residues in contact with GLY 445 (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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409C ASP* 6.2 1.3 - - - +
410C ILE 4.6 0.4 + - - -
443C LEU* 3.3 9.6 + - - +
444C LEU* 1.3 74.5 - - - +
446C ASP* 1.3 57.3 + - - +
461C ARG* 3.2 31.3 + - - -
462C ALA* 3.3 28.5 + - - +
463C ASP* 4.7 2.3 + - - -
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Residues in contact with ASP 446 (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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361C TYR* 2.5 29.9 + - - +
363C GLN* 4.4 0.2 + - - -
409C ASP* 3.7 3.8 - - - +
410C ILE* 2.8 34.7 + - + +
444C LEU* 3.2 6.4 - - + +
445C GLY* 1.3 78.8 - - - +
447C ARG* 1.3 62.4 + - - +
458C PHE* 3.4 20.0 - - + -
460C GLY 4.0 2.7 - - - -
461C ARG* 3.1 18.4 + - - -
462C ALA* 5.6 0.2 - - - -
1571C AMP 2.7 44.6 + - - -
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Residues in contact with ARG 447 (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 GLU* 2.8 49.8 + - - +
408C GLY* 3.3 15.6 + - - -
409C ASP* 3.0 33.6 + - - -
410C ILE* 3.6 8.6 - - - +
446C ASP* 1.3 75.6 - - - +
448C GLY* 1.3 57.8 + - - +
458C PHE* 3.9 3.1 - - - -
459C MET* 3.0 29.4 + - + +
460C GLY 3.0 21.7 + - - +
461C ARG 4.9 0.4 - - - +
462C ALA* 4.3 19.7 - - + +
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Residues in contact with GLY 448 (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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394C ILE* 3.6 10.0 - - - +
407C GLU* 3.6 4.2 - - - +
408C GLY 2.9 31.9 + - - +
410C ILE* 3.7 16.9 - - - +
447C ARG* 1.3 75.4 - - - +
449C ILE* 1.3 62.4 + - - -
457C GLN 3.2 13.2 - - - -
459C MET* 3.9 6.0 - - - +
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Residues in contact with ILE 449 (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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382C TYR* 6.0 0.9 - - + -
394C ILE* 4.1 3.8 - - - -
405C GLY* 3.5 32.5 - - - +
406C THR 4.1 4.3 - - - +
407C GLU* 4.1 20.4 - - + +
448C GLY* 1.3 78.5 - - - +
450C LYS* 1.3 70.7 + - - +
451C ASP* 4.2 3.1 - - + +
456C PHE* 3.6 5.4 - - - +
457C GLN* 2.9 58.7 + - + +
459C MET* 4.1 25.4 - - + -
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Residues in contact with LYS 450 (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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392C VAL 5.0 1.3 - - - +
393C GLN* 3.3 26.8 + - - +
394C ILE* 4.0 19.4 - - + +
401C VAL* 5.2 1.4 - - - +
402C LEU 4.5 14.5 + - - -
403C PRO 5.0 1.3 + - - +
404C PRO* 3.1 20.6 - - + +
405C GLY 2.6 31.6 + - - +
406C THR 4.9 1.4 + - - +
449C ILE* 1.3 78.3 - - - +
451C ASP* 1.3 58.2 + - - +
454C GLY* 3.6 33.0 - - - -
455C TYR 3.5 4.3 - - - +
456C PHE* 3.8 25.4 - - + -
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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