Contacts of the strand formed by residues 204 - 211 (chain E) in PDB entry 2F53
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 HIS 204 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E TRP 5.2 0.8 + - - -
158E VAL* 3.4 6.2 - - - +
159E ASN* 2.8 46.5 + - - +
160E GLY 4.9 5.9 + - - -
202E ARG 3.7 0.2 + - - -
203E ASN* 1.3 73.6 - - - +
205E PHE* 1.3 63.4 + - - +
206E ARG* 3.8 28.8 - - + +
235E GLU* 2.7 32.3 + - - +
236E ALA 3.9 3.6 - - - -
237E TRP* 3.2 53.5 - + + -
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Residues in contact with PHE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 5.8 1.1 - - + -
140E LEU* 3.6 22.7 - - + -
156E TRP* 4.9 5.4 - - + -
157E TRP 3.6 3.1 - - - -
158E VAL* 3.9 19.1 - - + -
191E LEU* 3.9 11.0 - - + -
193E VAL* 4.2 16.2 - - + -
197E PHE* 3.7 42.4 - + - -
198E TRP* 3.7 35.7 - + - -
203E ASN* 3.7 26.0 - - + -
204E HIS* 1.3 74.6 + - - +
206E ARG* 1.3 61.3 + - - +
235E GLU* 3.2 6.1 - - - +
236E ALA* 2.8 45.1 + - + +
238E GLY* 3.8 4.5 - - - -
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Residues in contact with ARG 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 5.4 0.2 - - - -
155E SER 3.7 0.3 - - - +
156E TRP* 3.4 10.0 - - - -
157E TRP* 2.7 79.3 + - + +
160E GLY* 6.1 1.2 - - - -
204E HIS* 3.8 22.4 - - + -
205E PHE* 1.3 76.0 - - - +
207E CYS* 1.3 66.2 + - - +
208E GLN* 2.5 37.7 + - - +
231E ILE* 4.5 6.1 - - - +
233E SER* 3.7 19.0 + - - -
234E ALA 3.5 11.7 - - - +
235E GLU* 4.2 8.3 - - + -
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Residues in contact with CYS 207 (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* 4.2 3.8 - - + +
124E VAL* 3.7 15.6 - - + +
142E CYS* 2.0 53.6 - - + -
154E LEU* 3.7 25.6 - - - -
155E SER 3.5 3.6 - - - -
156E TRP* 4.0 10.0 - - + -
206E ARG* 1.3 72.5 - - - +
208E GLN* 1.3 62.6 + - - +
209E VAL* 4.5 1.3 - - - -
232E VAL 4.3 0.2 - - - +
233E SER* 3.0 20.5 - - - -
234E ALA 3.0 13.4 + - - +
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Residues in contact with GLN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E GLU 3.6 2.1 + - - +
154E LEU* 3.3 3.5 - - - +
155E SER* 2.8 66.7 + - - +
157E TRP* 3.4 24.7 + - + +
206E ARG* 2.5 41.4 + - - +
207E CYS* 1.3 73.8 - - - +
209E VAL* 1.3 64.7 + - - +
210E GLN* 5.2 7.7 - - - +
231E ILE* 3.8 29.6 - - + +
233E SER* 3.7 9.6 - - - -
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E PRO* 4.0 14.8 - - + -
122E VAL* 3.8 26.5 - - + -
144E ALA* 4.1 10.5 - - + -
152E VAL* 3.7 36.6 - - + -
153E GLU 3.4 4.9 - - - +
154E LEU* 3.8 26.9 - - + +
187E LEU* 6.1 0.2 - - + -
207E CYS* 4.5 0.7 - - - -
208E GLN* 1.3 80.2 - - - +
210E GLN* 1.3 60.4 + - - +
211E PHE* 3.4 3.8 + - - +
230E GLN 3.7 0.3 - - - +
231E ILE* 3.5 2.4 - - - -
232E VAL* 2.9 37.2 + - - +
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Residues in contact with GLN 210 (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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151E HIS 3.8 0.2 - - - +
152E VAL* 3.1 7.8 - - - +
153E GLU* 2.9 42.6 + - + +
208E GLN* 4.1 8.7 - - - +
209E VAL* 1.3 71.7 - - - +
211E PHE* 1.3 78.1 + - - +
212E TYR* 3.4 36.9 + - + +
229E THR* 3.7 10.9 - - - +
230E GLN* 3.2 13.8 - - - +
231E ILE* 3.2 31.6 - - + +
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Residues in contact with PHE 211 (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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117E VAL* 4.0 8.5 - - + -
118E PHE 3.2 24.7 - - - -
119E PRO* 3.8 18.6 - - + -
120E PRO* 3.5 30.3 - - + -
147E PHE* 4.3 2.2 - - + -
148E TYR 3.5 9.9 - - - -
149E PRO* 3.8 20.6 - - + -
151E HIS 3.5 12.3 - - - -
152E VAL* 4.0 8.7 - - + -
209E VAL 3.4 0.6 + - - -
210E GLN* 1.3 81.1 - - - +
212E TYR* 1.3 71.1 + - - +
213E GLY* 3.6 17.0 - - - -
227E PRO 3.6 12.6 - - - -
228E VAL 3.6 16.2 - - - -
229E THR* 3.3 1.7 - - - +
230E GLN* 2.7 40.6 + - + +
232E VAL* 5.5 0.2 - - + -
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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
------------------------------------------------------------
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