Contacts of the helix formed by residues 1550 - 1558 (chain I) 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 ASN1550 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1547I PRO* 4.7 6.8 - - - +
1549I THR* 1.3 76.6 + - - +
1551I GLU* 1.3 67.4 + - - +
1552I PRO* 3.3 3.1 - - - -
1553I TYR* 3.0 9.3 + - - +
1554I ALA* 3.0 17.9 + - - -
1564I HIS* 3.0 27.2 + - - +
1565I VAL* 4.9 1.9 - - + +
1578I THR* 3.1 12.9 + - - -
1579I ILE 2.9 28.7 + - - -
1580I THR* 3.6 26.7 + - - +
1581I HIS* 3.7 22.2 + - + +
1618I PRO* 4.1 8.1 - - - +
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Residues in contact with GLU1551 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202I GLN* 3.7 24.8 + - - +
1227I ARG* 3.1 34.1 + - - -
1549I THR* 4.3 13.8 + - - +
1550I ASN* 1.3 76.2 - - - +
1552I PRO* 1.3 65.2 - - + +
1554I ALA* 3.0 9.0 + - - +
1555I ARG* 2.8 42.8 + - - +
1565I VAL* 3.4 25.8 - - + +
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Residues in contact with PRO1552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303I ALA* 4.5 12.8 - - + +
1547I PRO* 5.9 3.4 - - + -
1549I THR* 3.0 25.4 - - + +
1550I ASN 3.5 2.2 - - - -
1551I GLU* 1.3 93.9 - - + +
1553I TYR* 1.3 64.2 + - - +
1555I ARG* 3.4 7.6 + - + +
1556I VAL* 3.1 23.6 + - - +
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Residues in contact with TYR1553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1300I PHE* 4.4 12.5 - + - -
1303I ALA* 4.5 12.4 + - + +
1304I VAL* 3.9 31.0 - - + -
1327I ILE* 3.9 15.6 - - - +
1547I PRO* 5.9 3.6 - - + +
1549I THR 5.4 0.4 + - - -
1550I ASN* 3.0 10.0 + - - +
1552I PRO* 1.3 77.9 - - - +
1554I ALA* 1.3 64.7 + - - +
1555I ARG 3.2 0.2 + - - -
1556I VAL* 3.3 3.7 + - + +
1557I SER* 2.9 52.9 + - - -
1559I ASP* 5.0 2.5 - - + -
1581I HIS* 3.5 31.6 - + + +
1583I MET* 3.0 38.1 + - + +
1584I PHE* 4.1 29.4 - + + -
1587I ALA* 5.4 0.4 - - + -
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Residues in contact with ALA1554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550I ASN 3.0 13.1 + - - +
1551I GLU* 3.0 11.9 + - - +
1553I TYR* 1.3 76.4 - - - +
1555I ARG* 1.3 58.7 + - - +
1557I SER* 3.6 5.6 - - - -
1558I GLY* 3.0 26.7 + - - -
1559I ASP 3.3 27.0 + - - +
1560I LEU* 3.9 13.6 - - + +
1565I VAL* 4.6 9.9 - - + -
1581I HIS* 3.8 11.6 - - + -
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Residues in contact with ARG1555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202I GLN* 3.3 28.7 - - - +
1227I ARG* 4.1 16.2 - - - +
1228I THR 3.6 24.2 + - - +
1551I GLU* 2.8 24.9 + - - +
1552I PRO* 3.8 6.7 - - + +
1553I TYR 3.2 0.2 - - - -
1554I ALA* 1.3 80.8 - - - +
1556I VAL* 1.3 63.0 + - + +
1557I SER 3.5 0.2 + - - -
1558I GLY* 4.0 4.7 + - - -
1560I LEU* 4.2 18.4 - - - +
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Residues in contact with VAL1556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1296I GLU* 4.1 5.4 - - + +
1299I ASP* 3.8 18.6 - - + +
1300I PHE* 3.4 46.2 - - + +
1303I ALA* 3.5 23.1 - - + -
1325I PHE* 5.4 0.9 - - + -
1328I VAL* 2.9 22.8 - - + +
1552I PRO 3.1 19.5 - - - +
1553I TYR* 3.3 4.2 + - + +
1555I ARG* 1.3 77.7 - - + +
1557I SER* 1.3 59.7 + - - +
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Residues in contact with SER1557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1300I PHE* 5.2 2.7 - - - -
1327I ILE* 4.9 3.9 - - - +
1328I VAL* 3.9 18.9 - - - +
1331I TRP* 4.3 19.4 - - - +
1332I ARG* 5.5 1.0 + - - -
1553I TYR* 2.9 55.5 + - - -
1554I ALA* 3.4 1.4 + - - -
1556I VAL* 1.3 79.3 - - - +
1558I GLY* 1.3 61.9 + - - +
1559I ASP* 3.3 16.7 + - - +
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Residues in contact with GLY1558 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270I TRP* 3.3 20.8 - - - -
1331I TRP* 4.1 5.7 + - - -
1332I ARG* 4.1 24.5 + - - -
1554I ALA 3.0 8.8 + - - -
1555I ARG 4.0 3.4 + - - -
1556I VAL 3.6 1.8 - - - -
1557I SER* 1.3 78.5 - - - +
1559I ASP* 1.3 59.1 + - - +
1560I LEU* 3.3 20.1 - - - +
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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