Contacts of the helix formed by residues 152 - 158 (chain B) in PDB entry 3P4P
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 GLY 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 4.0 10.3 - - - +
96B PHE* 4.9 0.2 - - - -
106B MET* 4.7 5.4 - - - -
109B PHE* 3.8 25.3 - - - -
148B CYS* 6.1 0.2 - - - -
150B ASN 3.3 4.8 + - - -
151B CYS* 1.3 80.3 - - - +
153B LEU* 1.3 65.6 + - - +
154B CYS* 3.0 8.9 - - - -
155B TYR* 2.9 21.5 + - - +
156B ALA 3.3 8.3 + - - -
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Residues in contact with LEU 153 (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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66B GLY* 4.0 11.4 - - - -
73B PRO* 3.5 14.4 - - + +
74B LYS* 3.5 46.2 - - - +
75B LEU* 3.9 8.3 - - + +
93B LEU* 3.7 24.2 - - + -
151B CYS* 3.3 25.2 - - + +
152B GLY* 1.3 76.9 - - - +
154B CYS* 1.3 55.2 + - - +
156B ALA* 3.3 3.3 + - - +
157B ALA* 2.9 30.0 + - - +
213B VAL* 3.5 31.1 - - + +
214B CYS* 5.5 0.4 - - - -
215B PRO* 4.0 10.1 - - + -
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Residues in contact with CYS 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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148B CYS* 5.2 6.3 - - - -
151B CYS* 5.0 6.5 - - - -
152B GLY* 3.0 6.4 - - - -
153B LEU* 1.3 83.7 - - - +
155B TYR* 1.3 60.3 + - - +
157B ALA* 3.1 4.6 + - - +
158B CYS* 2.9 32.1 + - - +
170B PRO* 3.5 25.7 - - + +
171B ALA* 3.9 30.3 - - - -
210B CYS* 4.0 19.3 - - + +
213B VAL* 4.2 2.1 - - - +
214B CYS* 5.5 7.1 - - - +
220B PRO* 4.8 10.5 - - + -
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Residues in contact with TYR 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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94B ALA 4.4 0.2 - - - -
95B ASN* 2.7 21.5 + - - -
96B PHE* 3.3 26.5 - + + -
108B HIS* 4.8 5.6 - + - -
109B PHE* 3.1 43.3 - + - -
112B SER* 4.6 0.5 - - - -
113B LEU* 4.4 0.9 - - - +
152B GLY* 2.9 8.5 + - - +
154B CYS* 1.3 75.5 - - + +
156B ALA* 1.3 61.0 + - - +
157B ALA 3.1 1.7 + - - -
158B CYS* 3.6 7.1 + - - +
161B PHE* 3.3 46.3 - + + -
167B PHE 4.5 0.2 - - - -
168B ILE 2.6 31.1 + - - -
169B GLY* 3.4 12.9 - - - -
170B PRO* 3.6 12.3 - - + -
171B ALA* 3.6 14.2 - - + +
172B ALA* 2.9 23.7 + - - +
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Residues in contact with ALA 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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68B MET* 3.9 5.2 - - - +
73B PRO* 3.7 19.2 - - + +
93B LEU* 3.5 28.3 - - + -
94B ALA* 3.3 34.4 + - + +
95B ASN* 3.0 14.1 + - - +
96B PHE* 4.4 0.2 - - - -
152B GLY 3.3 5.3 + - - -
153B LEU 3.8 2.2 - - - +
155B TYR* 1.3 78.9 - - - +
157B ALA* 1.3 59.9 + - - +
22C TYR* 4.3 5.0 + - - -
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Residues in contact with ALA 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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73B PRO* 4.1 5.8 - - + -
153B LEU 2.9 17.5 + - - +
154B CYS 3.1 5.3 + - - +
156B ALA* 1.3 80.2 - - - +
158B CYS* 1.3 57.6 + - - +
159B PRO* 3.1 7.8 - - - +
209B TYR* 3.4 37.6 - - + +
210B CYS* 4.2 2.7 - - - -
213B VAL* 3.8 17.7 - - + -
22C TYR* 2.7 22.1 + - - -
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Residues in contact with CYS 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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95B ASN* 3.6 8.9 + - - -
154B CYS 2.9 15.1 + - - +
155B TYR 3.6 0.6 + - - +
156B ALA 3.3 1.0 - - - -
157B ALA* 1.3 75.8 - - - +
159B PRO* 1.3 69.1 - - - +
160B GLN* 3.0 29.4 - - - -
161B PHE* 3.0 27.4 + - + +
162B GLY 3.2 7.8 + - - -
167B PHE* 3.8 16.4 - - - -
170B PRO* 4.4 11.4 - - + -
204B CYS* 5.7 5.8 - - - -
207B VAL* 5.8 2.0 - - - -
209B TYR* 5.8 0.4 - - - -
210B CYS* 5.7 5.8 - - + +
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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