Contacts of the strand formed by residues 230 - 237 (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 GLN 230 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E PRO* 3.6 28.6 - - - +
210E GLN* 3.9 4.0 - - - -
211E PHE* 2.9 37.7 + - + +
226E LYS 4.4 2.4 + - - -
227E PRO* 4.1 2.8 - - - +
228E VAL* 2.9 35.8 + - + +
229E THR* 1.3 75.8 - - - +
231E ILE* 1.3 66.1 + - - +
232E VAL* 3.7 21.8 + - + +
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Residues in contact with ILE 231 (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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206E ARG* 3.9 22.9 - - - +
208E GLN* 3.9 31.9 - - + +
209E VAL 3.4 9.2 - - - +
210E GLN* 3.3 32.5 - - + +
230E GLN* 1.3 77.9 - - - +
232E VAL* 1.3 68.2 + - - +
233E SER* 4.4 1.7 + - - +
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Residues in contact with VAL 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E PRO* 4.9 0.9 - - + -
120E PRO* 3.7 37.7 - - + +
121E GLU* 4.8 0.7 - - - -
122E VAL* 3.7 27.0 - - + +
209E VAL* 2.7 37.0 + - - +
230E GLN* 3.7 29.2 - - + +
231E ILE* 1.3 77.3 - - - +
233E SER* 1.3 66.2 + - - +
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Residues in contact with SER 233 (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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122E VAL* 4.4 8.2 - - - +
206E ARG* 3.4 33.2 + - - -
207E CYS 3.1 16.6 - - - -
208E GLN* 3.8 7.4 - - - -
231E ILE* 4.2 2.3 - - - +
232E VAL* 1.3 81.9 - - - +
234E ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 234 (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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129D SER* 5.9 0.2 - - - +
122E VAL* 3.5 26.4 - - + +
123E ALA* 3.7 11.4 - - - -
124E VAL* 3.6 23.8 - - + +
206E ARG* 3.6 2.1 - - - +
207E CYS 2.9 28.7 + - - +
233E SER* 1.3 74.4 - - - +
235E GLU* 1.3 64.5 + - - +
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Residues in contact with GLU 235 (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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129D SER* 3.1 19.6 + - - -
124E VAL* 4.1 4.9 - - - +
204E HIS* 2.8 37.2 + - + +
205E PHE 3.2 12.8 - - - +
206E ARG* 4.1 13.4 - - + -
234E ALA* 1.3 78.1 - - - +
236E ALA* 1.3 61.6 + - - +
237E TRP* 4.6 10.2 + - + +
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Residues in contact with ALA 236 (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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129D SER* 4.0 20.4 - - - -
124E VAL* 4.0 16.8 - - + -
126E GLU* 4.2 12.8 - - + +
140E LEU* 4.5 10.8 - - + -
198E TRP* 4.5 4.0 - - + -
204E HIS* 3.8 1.4 - - - -
205E PHE* 2.8 36.0 + - - +
235E GLU* 1.3 76.6 - - - +
237E TRP* 1.3 68.0 + - - +
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Residues in contact with TRP 237 (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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126E GLU* 4.6 3.3 + - - +
198E TRP* 3.5 16.7 - - - -
201E PRO 3.8 18.4 - - - +
202E ARG* 3.9 13.2 - - - -
203E ASN 3.3 7.4 - - - -
204E HIS* 3.2 48.7 + + + -
205E PHE* 4.6 0.2 - - - -
235E GLU* 4.6 11.4 + - + -
236E ALA* 1.3 83.0 - - - +
238E GLY* 1.3 71.3 + - - +
239E ARG* 4.3 5.2 - - - +
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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