Contacts of the strand formed by residues 152 - 158 (chain E) in PDB entry 2P5W
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 VAL 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E PHE* 4.7 4.1 - - - -
120E PRO* 4.7 0.9 - - + -
147E PHE* 3.7 47.1 - - + -
150E ASP* 3.8 8.5 + - - +
151E HIS* 1.3 79.8 - - - +
153E GLU* 1.3 69.9 + - - +
154E LEU 4.2 0.2 - - - -
173E PRO* 6.0 0.4 - - + -
187E LEU* 4.2 20.2 - - + -
209E VAL* 3.8 23.6 - - + -
210E GLN 3.1 8.1 - - - +
211E PHE* 3.9 14.6 - - + -
212E TYR* 4.8 1.1 - - - -
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Residues in contact with GLU 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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8E PHE* 3.9 17.3 - - + -
152E VAL* 1.3 80.1 - - - +
154E LEU* 1.3 61.3 + - - +
155E SER* 4.0 2.0 + - - -
208E GLN* 3.6 3.6 + - - +
209E VAL* 4.5 0.7 - - - -
210E GLN* 2.9 39.3 + - + +
212E TYR* 2.8 35.4 + - + -
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Residues in contact with LEU 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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142E CYS* 4.2 4.7 - - + -
144E ALA* 5.2 1.6 - - + -
152E VAL* 4.2 0.8 - - + +
153E GLU* 1.3 72.5 - - - +
155E SER* 1.3 74.0 + - - +
156E TRP* 4.0 10.3 - - + +
169E THR* 3.9 14.2 + - + +
187E LEU* 4.1 37.3 - - + +
189E SER* 3.6 40.2 - - - +
207E CYS* 4.0 22.2 - - - -
208E GLN 3.4 4.0 - - - +
209E VAL* 4.1 15.9 - - + +
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Residues in contact with SER 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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153E GLU 5.0 1.5 + - - -
154E LEU* 1.3 80.2 - - - +
156E TRP* 1.3 62.6 + - - +
157E TRP* 2.9 25.6 + - - -
162E GLU* 3.6 24.0 - - - -
207E CYS* 3.5 3.8 - - - -
208E GLN* 2.9 48.5 + - - +
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Residues in contact with TRP 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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124E VAL* 4.7 7.4 - - + -
140E LEU* 4.0 29.4 - - + -
141E VAL 4.2 1.3 - - - -
142E CYS* 3.4 42.6 - - + -
154E LEU* 4.0 5.6 - - + +
155E SER* 1.3 74.5 - - - +
157E TRP* 1.3 63.1 + - - +
158E VAL 4.2 0.2 - - - -
162E GLU* 3.3 8.5 - - - +
163E VAL* 3.0 47.1 + - + +
167E VAL* 3.6 31.0 - - + -
189E SER* 2.7 25.9 + - - -
190E ARG 3.8 4.4 + - - -
191E LEU* 3.5 38.8 - - + -
205E PHE* 4.9 3.1 - - + -
206E ARG 3.5 20.0 - - - -
207E CYS* 4.0 15.9 - - + -
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Residues in contact with TRP 157 (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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155E SER* 2.9 27.5 + - - -
156E TRP* 1.3 76.3 - - - +
158E VAL* 1.3 62.5 + - - +
159E ASN 4.1 0.6 + - - -
160E GLY* 3.5 23.7 + - - -
161E LYS* 3.4 10.8 - - - +
162E GLU* 3.2 50.3 - - + -
204E HIS* 3.5 4.0 + - - +
205E PHE* 3.6 0.3 - - - -
206E ARG* 2.8 71.9 + - + +
208E GLN* 3.4 26.2 - - + -
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Residues in contact with VAL 158 (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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156E TRP 4.2 0.4 - - - -
157E TRP* 1.3 73.4 - - - +
159E ASN* 1.3 81.6 + - - +
160E GLY 3.2 0.4 - - - -
161E LYS* 2.9 23.5 + - - +
163E VAL* 4.0 24.3 - - + +
191E LEU* 3.8 18.2 - - + -
193E VAL* 5.7 1.1 - - + -
197E PHE* 3.7 34.8 - - + -
204E HIS 3.2 9.2 - - - +
205E PHE* 3.6 27.1 - - + -
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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