Contacts of the strand formed by residues 1572 - 1575 (chain B) in PDB entry 2VKZ
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 VAL1572 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536B LEU* 3.9 16.4 - - + +
1537B GLY 3.6 7.0 - - - +
1539B ALA* 3.9 26.9 - - + +
1541B PHE* 4.7 0.7 - - + -
1557B ILE* 4.0 17.0 - - + -
1561B MET* 3.9 27.1 - - + -
1566B ARG* 3.4 19.3 - - - +
1571B PRO* 1.3 72.9 - - - +
1573B ILE* 1.3 61.0 + - - +
1574B GLY 3.6 0.5 + - - -
1623B TYR 2.8 18.2 + - - +
1624B VAL* 4.3 11.7 - - + -
1625B LEU* 2.9 24.6 + - - +
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Residues in contact with ILE1573 (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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414B LEU* 3.7 25.4 - - + -
418B PHE* 6.0 0.9 - - + -
454B HIS* 6.2 2.5 - - + -
1537B GLY 3.0 14.9 + - - +
1538B VAL* 3.2 11.7 - - + +
1539B ALA 2.8 21.5 + - - -
1571B PRO* 4.5 6.5 - - + +
1572B VAL* 1.3 73.2 - - - +
1574B GLY* 1.3 58.2 + - - +
1605B ILE* 3.8 42.2 - - + -
1625B LEU* 3.7 19.7 - - + -
1627B PRO* 3.3 30.3 - - + -
1631B LEU* 4.5 4.5 - - + -
1633B THR* 5.8 0.7 - - + -
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Residues in contact with GLY1574 (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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1539B ALA 3.1 11.9 - - - -
1541B PHE* 3.7 18.1 - - - -
1572B VAL 3.6 3.6 + - - -
1573B ILE* 1.3 71.7 - - - +
1575B VAL* 1.3 63.6 + - - +
1576B PHE* 3.4 14.4 - - - -
1606B PRO 5.4 0.3 - - - +
1608B ASN* 5.4 0.5 + - - +
1624B VAL* 5.1 0.4 - - - +
1625B LEU 3.1 12.9 + - - +
1627B PRO* 3.1 24.1 - - - +
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Residues in contact with VAL1575 (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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1040B GLU* 5.3 5.6 - - - +
1538B VAL* 3.8 13.2 - - + -
1539B ALA 3.1 2.6 + - - -
1540B SER* 3.5 32.8 - - - +
1541B PHE* 3.0 26.2 + - - +
1574B GLY* 1.3 74.6 - - - -
1576B PHE* 1.3 69.3 + - - +
1577B GLN* 4.7 8.3 - - + +
1599B ILE* 4.1 13.5 - - + -
1605B ILE* 3.7 28.7 - - + -
1606B PRO* 4.1 15.9 - - + +
1608B ASN 5.7 2.5 - - - +
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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