Contacts of the helix formed by residues 153 - 160 (chain B) in PDB entry 2F4W
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 ASP 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 3.6 24.1 + - - -
81B ILE* 4.6 7.8 - - - +
149B PHE* 3.7 15.3 + - + +
150B ASN* 3.1 14.3 + - - +
151B LEU 3.2 0.6 - - - -
152B LYS* 1.3 75.7 - - - +
154B LYS* 1.3 63.9 + - - +
155B VAL* 3.0 22.5 + - - +
156B PHE* 3.1 13.7 + - + +
157B CYS* 3.0 23.9 + - - -
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Residues in contact with LYS 154 (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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152B LYS 3.7 4.2 + - - -
153B ASP* 1.3 70.4 + - - +
155B VAL* 1.3 62.5 + - + +
157B CYS* 3.8 7.7 - - + +
158B GLU* 2.8 58.8 + - + +
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Residues in contact with VAL 155 (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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37B LEU* 5.0 4.7 - - + -
45B HIS* 4.1 22.7 - - + +
62B HIS* 4.7 2.9 - - + -
153B ASP* 3.0 10.4 + - - +
154B LYS* 1.3 77.7 - - + +
156B PHE* 1.3 67.6 + - - +
158B GLU* 3.9 3.7 - - - +
159B LEU* 3.1 44.5 + - + +
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Residues in contact with PHE 156 (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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47B VAL* 3.7 25.8 - - + -
62B HIS* 3.9 29.8 - + + +
150B ASN* 3.4 44.9 - - + +
151B LEU* 4.7 1.1 - - + -
153B ASP* 3.1 23.3 + - + +
155B VAL* 1.3 79.0 - - - +
157B CYS* 1.3 64.0 + - - +
160B PHE* 2.9 42.3 + + + +
163B VAL* 3.7 17.3 - - + -
164B VAL* 3.7 22.9 - - + -
167B ILE* 3.7 26.9 - - + -
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Residues in contact with CYS 157 (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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150B ASN 3.8 7.4 - - - -
151B LEU* 3.4 29.2 - - - -
153B ASP 3.0 17.9 + - - +
154B LYS* 3.8 8.5 - - + +
156B PHE* 1.3 81.9 - - - +
158B GLU* 1.3 61.9 + - - +
161B PRO* 3.6 25.1 - - - +
164B VAL* 3.6 26.6 - - + +
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Residues in contact with GLU 158 (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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38B PRO* 6.0 1.4 - - - +
154B LYS* 2.8 43.1 + - - +
155B VAL* 4.0 3.8 - - - +
157B CYS* 1.3 80.0 - - - +
159B LEU* 1.3 68.0 + - + +
161B PRO* 3.9 8.0 - - - +
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Residues in contact with LEU 159 (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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35B GLU* 3.5 35.8 - - + +
36B PRO 4.4 7.0 - - - +
37B LEU* 3.7 15.7 - - + -
38B PRO* 4.1 26.5 - - + -
45B HIS* 3.7 37.5 - - + -
155B VAL* 3.1 27.3 + - + +
158B GLU* 1.3 85.0 - - + +
160B PHE* 1.3 70.7 + - + +
161B PRO* 3.3 9.4 - - - +
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Residues in contact with PHE 160 (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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33B CYS* 3.7 40.2 - - + -
35B GLU* 3.9 20.9 - - + -
45B HIS* 3.6 43.7 - - + -
46B TYR* 3.7 4.7 - - - -
47B VAL* 3.5 23.1 - - + -
62B HIS* 4.0 10.8 - + - -
156B PHE* 2.9 29.0 + + + +
157B CYS 3.9 3.6 - - - -
159B LEU* 1.3 90.5 - - + +
161B PRO* 1.3 63.7 - - - +
162B GLU 3.3 2.7 - - - -
163B VAL* 2.9 27.5 + - + -
164B VAL* 3.0 13.5 + - - +
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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