Contacts of the helix formed by residues 605 - 610 (chain C) in PDB entry 2W4V
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 ASN 605 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C ALA* 3.8 26.6 - - + +
401C PRO* 3.0 31.3 - - - +
402C LYS* 2.8 43.6 + - - +
603C ASN* 2.6 7.1 + - + +
604C GLU* 1.3 80.6 - - - +
606C VAL* 1.3 56.9 + - - +
607C VAL 3.1 0.9 - - - -
608C ALA* 2.8 33.7 + - - +
609C LEU* 3.2 6.4 + - - +
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Residues in contact with VAL 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 4.3 21.8 - - + -
397C ALA* 4.5 2.0 - - + +
398C LEU* 4.9 2.0 - - + -
426C LEU* 3.4 36.3 - - + -
603C ASN* 1.5 69.4 + - - +
605C ASN* 1.3 76.3 - - - +
607C VAL* 1.3 59.2 + - + +
608C ALA 3.0 0.2 - - - -
609C LEU* 3.1 10.8 + - + +
610C LEU* 3.0 40.4 + - + +
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Residues in contact with VAL 607 (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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426C LEU* 5.5 1.1 - - + -
602C ILE* 3.3 38.1 - - + -
603C ASN 3.4 3.6 - - - +
604C GLU* 2.3 52.0 - - + +
606C VAL* 1.3 78.5 - - + +
608C ALA* 1.3 56.5 + - + +
610C LEU* 4.5 4.6 - - - +
611C GLY* 3.0 22.7 + - - -
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Residues in contact with ALA 608 (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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604C GLU 4.0 7.9 - - - +
605C ASN* 2.8 15.6 + - - +
607C VAL* 1.3 80.9 - - - +
609C LEU* 1.3 65.0 + - - +
611C GLY* 3.0 10.1 + - - -
612C ALA* 3.4 11.1 + - - +
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Residues in contact with LEU 609 (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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389C ILE* 3.7 15.6 - - + +
390C ASN 5.6 0.7 - - - +
393C ASP* 3.1 45.1 - - + +
394C LEU* 3.1 37.9 - - + +
397C ALA* 4.5 9.0 - - + -
605C ASN 3.2 7.6 + - - +
606C VAL* 3.1 12.3 + - + +
608C ALA* 1.3 82.7 - - + +
610C LEU* 1.3 62.4 + - + +
612C ALA* 3.2 11.4 + - - +
613C SER* 3.4 9.9 + - - -
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Residues in contact with LEU 610 (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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387C CYS* 3.8 16.6 - - + +
389C ILE* 3.6 25.8 - - + -
394C LEU* 6.2 0.9 - - + -
426C LEU* 5.9 3.8 - - + -
430C LEU* 4.0 35.9 - - + -
433C ARG* 4.9 8.5 - - - +
606C VAL* 3.0 24.7 + - + +
607C VAL* 4.5 4.0 - - - +
609C LEU* 1.3 74.9 - - + +
611C GLY* 1.3 66.0 + - - +
612C ALA 3.0 2.9 + - - -
613C SER* 3.2 28.5 + - - -
618C VAL* 3.7 25.2 - - + +
619C ALA* 3.8 1.2 - - - -
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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