Contacts of the helix formed by residues 162 - 171 (chain 4) in PDB entry 2WSF
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 ALA 162 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1584 ARG* 4.0 10.5 - - + +
1594 LEU 4.7 1.6 - - - +
1604 MET 3.3 1.4 + - - -
1614 LEU* 1.3 77.0 - - - +
1634 PHE* 1.3 54.6 + - - +
1644 LEU* 3.8 2.8 - - - +
1654 GLY* 3.4 11.5 - - - +
1664 PHE* 2.5 33.1 + - - +
3044 CLA 4.7 5.9 - - - +
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Residues in contact with PHE 163 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554 VAL* 4.6 14.1 - - + -
584 MET* 6.2 5.2 - - + -
1594 LEU* 2.9 27.3 + - + +
1604 MET* 2.9 53.8 + - + +
1624 ALA* 1.3 72.8 - - - +
1644 LEU* 1.3 52.4 + - - +
1664 PHE* 2.6 37.2 + + + +
1674 ILE* 2.3 44.5 + - + +
3064 CLA 4.8 2.5 - + + -
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Residues in contact with LEU 164 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514 ALA* 5.3 9.4 - - + -
544 GLY* 5.8 9.0 - - - -
554 VAL* 4.8 8.5 - - + +
1604 MET 2.9 16.9 + - - +
1614 LEU* 5.3 0.7 - - - -
1624 ALA 3.5 2.0 - - - +
1634 PHE* 1.3 68.3 - - - +
1654 GLY* 1.3 64.1 + - - +
1674 ILE* 2.4 37.0 + - + +
1684 ILE* 2.9 43.6 + - + -
3094 CLA 5.8 9.9 - - + +
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Residues in contact with GLY 165 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624 ALA* 3.4 15.6 + - - +
1634 PHE 3.2 0.6 - - - -
1644 LEU* 1.3 83.6 - - - +
1664 PHE* 1.3 49.0 + - - +
1684 ILE* 3.7 1.1 - - - -
1694 GLN* 2.6 38.4 + - - +
3044 CLA 3.5 26.2 - - - -
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Residues in contact with PHE 166 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624 ALA 2.5 17.6 + - - +
1634 PHE* 2.6 37.7 + + + +
1644 LEU 2.9 3.8 - - - -
1654 GLY* 1.3 66.1 - - - -
1674 ILE* 1.3 88.5 + - + +
1694 GLN* 2.6 35.5 + - - +
1704 HIS* 3.2 32.9 + + + -
1784 PHE* 6.3 2.5 - + - -
3044 CLA 4.0 2.4 - - - +
3074 CLA 3.4 41.1 - + + -
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Residues in contact with ILE 167 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554 VAL* 3.9 33.9 - - + -
584 MET* 4.6 26.2 - - + -
1634 PHE* 2.3 37.3 + - + +
1644 LEU* 2.4 16.7 + - + +
1664 PHE* 1.3 90.2 - - + +
1684 ILE* 1.3 73.9 + - + +
1694 GLN 2.9 2.6 + - - -
1704 HIS* 3.3 10.6 + - - +
1714 ASN* 3.7 8.5 + - - +
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Residues in contact with ILE 168 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644 LEU* 2.9 35.2 + - + +
1654 GLY* 3.7 3.1 - - - -
1674 ILE* 1.3 83.1 - - + +
1694 GLN* 1.3 71.3 + - - +
1714 ASN* 4.9 12.3 - - + +
1724 VAL* 4.8 6.6 - - + +
3044 CLA 4.3 7.1 - - + +
3094 CLA 3.4 41.1 - - + -
3114 CLA 6.5 0.4 - - + -
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Residues in contact with GLN 169 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654 GLY* 2.6 16.7 + - - +
1664 PHE* 2.6 26.9 + - - +
1684 ILE* 1.3 85.1 + - - +
1704 HIS* 1.3 73.0 + - + +
1714 ASN 3.5 0.7 - - - -
1724 VAL* 3.9 18.0 - - - +
1734 THR* 5.4 0.7 - - - +
3044 CLA 2.6 71.0 - - + +
42J PHE 5.4 1.9 - - - +
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Residues in contact with HIS 170 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664 PHE* 3.2 48.1 + + + +
1674 ILE 3.3 2.6 + - - +
1694 GLN* 1.3 86.1 - - + +
1714 ASN* 1.3 74.4 - - - +
1734 THR* 2.8 27.2 - - + +
1744 GLY* 4.3 1.8 - - - -
1754 LYS 5.8 0.2 - - - -
3074 CLA 4.6 9.9 - + + -
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Residues in contact with ASN 171 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694 ILE* 3.5 36.2 - - + +
704 ILE* 4.6 9.9 - - - +
1674 ILE 3.7 10.5 + - - +
1684 ILE* 4.9 11.8 - - + +
1704 HIS* 1.3 89.4 - - - +
1724 VAL* 1.3 73.4 + - + +
1734 THR* 1.8 28.9 + - - -
1744 GLY* 4.4 11.3 + - - +
1754 LYS* 5.4 3.1 - - + +
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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