Contacts of the helix formed by residues 1561 - 1565 (chain H) 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 ASN1561 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266H TYR* 3.1 32.6 + - - -
1269H LEU* 5.6 0.4 - - - -
1270H TRP* 3.9 16.9 - - + +
1347H LEU 5.3 2.2 + - - -
1350H LEU* 6.0 3.0 - - - +
1559H ASP* 3.1 20.1 + - - +
1560H LEU* 1.3 76.4 - - - +
1562H PRO* 1.4 69.3 - - - +
1563H ILE* 3.0 36.0 + - - +
1564H HIS* 3.3 28.6 + - + +
1565H VAL* 3.8 10.2 - - - +
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Residues in contact with PRO1562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225H GLU* 3.7 21.5 - - + +
1265H MET* 3.3 30.7 - - + -
1266H TYR* 4.0 15.3 - - + +
1269H LEU* 4.2 3.6 - - + -
1560H LEU 3.1 8.9 - - - +
1561H ASN* 1.4 88.2 - - - +
1563H ILE* 1.3 61.7 + - - +
1564H HIS 3.0 2.7 - - - -
1565H VAL* 3.0 2.6 + - + +
1566H SER 2.7 33.7 + - - +
1569H PHE* 3.1 33.7 - - + -
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Residues in contact with ILE1563 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266H TYR* 4.5 8.5 + - - +
1347H LEU 5.6 0.7 - - - +
1348H LEU* 3.9 26.5 - - + +
1350H LEU 5.5 6.1 - - - +
1561H ASN* 3.0 21.6 + - - +
1562H PRO* 1.3 78.0 - - - +
1564H HIS* 1.3 82.0 + - + +
1565H VAL 3.8 0.2 + - - -
1569H PHE* 4.2 7.3 - - + +
1570H ALA* 3.4 28.7 - - - +
1573H ALA* 4.2 10.5 - - + -
1575H LEU* 3.7 32.5 - - + -
1577H GLY 4.2 0.2 - - - +
1578H THR* 3.7 8.1 - - - +
1579H ILE* 4.1 6.1 + - + -
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Residues in contact with HIS1564 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550H ASN* 2.9 27.2 + - - +
1559H ASP* 4.7 4.2 + - - -
1561H ASN* 3.3 30.0 + - + +
1562H PRO 3.0 1.2 - - - -
1563H ILE* 1.3 91.6 - - + +
1565H VAL* 1.3 60.1 + - + +
1578H THR* 3.6 10.6 - - - -
1579H ILE* 2.6 36.0 + - + +
1580H THR 3.9 4.7 - - - -
1581H HIS* 3.2 62.6 + + + -
1582H GLY 4.6 2.9 + - - -
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Residues in contact with VAL1565 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225H GLU* 4.9 1.3 - - - +
1227H ARG* 2.9 61.6 + - + +
1550H ASN* 4.9 3.1 - - + +
1551H GLU* 3.5 24.0 - - + +
1554H ALA* 4.6 20.2 - - + -
1559H ASP 5.3 0.4 - - - +
1560H LEU* 5.2 4.3 - - - +
1561H ASN 3.8 15.7 - - - +
1562H PRO* 3.0 4.8 + - + +
1563H ILE 3.4 0.2 - - - -
1564H HIS* 1.3 90.3 - - + +
1566H SER* 1.3 62.5 + - - +
1567H ARG 3.8 2.1 + - - -
1578H THR* 4.1 7.1 - - - +
1581H HIS* 4.9 1.3 - - + -
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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