Contacts of the strand formed by residues 151 - 156 (chain E) in PDB entry 4DOH
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 ILE 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E LEU* 4.4 16.6 - - + -
145E THR 3.7 6.7 - - - +
146E THR* 3.8 19.7 - - + -
150E SER* 1.3 75.0 - - - +
152E SER* 1.3 75.5 + - - +
153E VAL* 4.4 10.1 - - + -
203E LEU 4.0 0.3 - - - +
204E VAL* 3.7 1.7 - - - +
205E LEU* 2.9 42.3 + - + +
208E LEU* 3.3 14.2 - - + +
214E TYR* 3.6 32.1 - - + +
216E VAL* 5.5 2.7 - - + -
237E ALA* 3.4 28.0 - - + +
239E THR* 4.4 7.2 - - + -
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Residues in contact with SER 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ALA 3.4 1.6 - - - +
144E LEU* 3.3 8.5 - - - -
145E THR* 2.8 48.3 + - - +
150E SER* 4.2 3.2 + - - -
151E ILE* 1.3 74.0 - - - +
153E VAL* 1.3 63.4 + - - +
154E VAL* 4.1 7.4 - - - -
202E THR* 6.1 1.1 - - - -
203E LEU 3.8 3.4 - - - -
204E VAL* 3.3 24.3 - - - +
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 4.9 5.8 - - + -
143E ALA 3.8 2.7 - - - +
144E LEU* 3.8 22.4 - - + -
151E ILE* 4.4 1.3 - - + -
152E SER* 1.3 76.7 - - - +
154E VAL* 1.3 66.3 + - - +
155E LEU* 4.1 21.8 - - + +
183E VAL* 5.0 7.2 - - + -
202E THR* 3.1 4.3 + - - -
203E LEU* 2.7 56.6 + - + +
205E LEU* 4.1 26.2 - - + -
216E VAL* 4.5 16.4 - - + -
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Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU 3.5 1.9 - - - +
142E VAL* 4.5 1.1 - - - -
143E ALA* 3.1 49.5 + - + +
145E THR* 5.3 7.6 - - + -
152E SER* 5.1 7.0 - - - +
153E VAL* 1.3 81.8 - - - +
155E LEU* 1.3 62.6 + - - +
156E THR* 5.4 1.9 - - + +
201E HIS 3.4 4.5 - - - +
202E THR* 3.6 21.5 - - + +
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO* 3.7 17.9 - - + -
141E GLU 3.0 10.8 - - - +
142E VAL* 4.4 3.6 - - + +
153E VAL* 4.3 16.2 - - + +
154E VAL* 1.3 76.4 - - - +
156E THR* 1.3 67.1 + - - +
157E ALA 4.2 0.2 - - - -
181E TYR* 4.1 20.4 - - + -
183E VAL* 4.4 8.3 - - + -
198E VAL* 4.8 4.9 - - + -
200E ASN 3.6 12.8 - - - +
201E HIS* 2.8 56.9 + - + +
202E THR* 4.4 1.1 - - - +
203E LEU* 6.3 1.6 - - + -
218E VAL* 3.7 37.7 - - + -
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Residues in contact with THR 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO* 3.4 3.6 - - - +
141E GLU* 2.7 68.1 + - - +
154E VAL* 4.0 1.8 + - + +
155E LEU* 1.3 78.6 - - - +
157E ALA* 1.3 68.9 + - - +
201E HIS* 4.9 3.8 - - - +
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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