Contacts of the strand formed by residues 191 - 196 (chain E) in PDB entry 5IJ7
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 LEU 191 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E PHE* 3.6 5.3 - - - -
185E HIS* 2.9 63.3 + - + +
188E ASP* 3.3 27.7 + - + +
189E PRO 3.5 0.2 - - - -
190E ASN* 1.3 76.1 - - - +
192E LEU* 1.3 60.1 + - - +
203E LEU* 4.0 15.3 - - + -
204E TRP 3.4 9.9 - - - +
205E ASN* 4.1 25.1 - - + +
212E VAL* 4.5 9.4 - - + -
230E TYR* 3.6 3.1 + - - -
260E ILE* 3.9 37.0 - - + -
264E TYR* 4.8 0.2 - - - +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ALA* 4.3 0.7 - - + -
158E ILE* 3.6 39.7 - - + -
160E ILE* 4.0 9.0 - - + -
182E LEU* 3.8 24.0 - - + -
183E LYS 3.6 16.6 - - - +
184E PHE* 3.7 34.8 - - + -
190E ASN 3.6 0.8 + - - -
191E LEU* 1.3 73.4 - - - +
193E LEU* 1.3 64.3 + - - +
202E ARG 3.4 2.4 - - - +
203E LEU* 3.4 1.8 - - - -
204E TRP* 2.8 41.0 + - + -
206E ILE* 3.7 26.5 - - + -
230E TYR* 4.1 1.6 - - - -
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E GLU 3.9 0.7 - - - +
182E LEU* 3.2 4.9 - - - -
183E LYS* 2.8 46.4 + - + +
192E LEU* 1.3 75.4 - - - +
194E SER* 1.3 61.4 + - - +
195E VAL* 4.6 6.4 - - + +
201E LEU* 4.1 22.7 - - + -
202E ARG 3.2 19.5 - - - +
203E LEU* 4.5 3.1 - - + +
215E PHE* 4.4 6.3 - - + -
228E ALA* 3.9 15.9 - - + -
229E ASP 5.0 2.0 - - - +
230E TYR* 3.4 23.7 + - + +
237E ILE* 3.6 49.6 - - + -
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Residues in contact with SER 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E ILE* 3.8 13.9 - - - -
175E HIS* 2.7 32.4 - - - -
179E ILE* 4.1 4.3 - - - -
181E GLU 3.4 4.9 - - - -
182E LEU* 3.8 19.1 - - - -
192E LEU* 4.1 0.4 + - - -
193E LEU* 1.3 74.1 - - - +
195E VAL* 1.3 62.2 + - - +
201E LEU* 3.3 5.2 - - - +
202E ARG 2.8 31.1 + - - -
204E TRP* 2.9 15.8 + - - -
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ILE* 3.4 4.2 - - - +
180E ASN* 2.8 27.5 + - - +
181E GLU* 2.9 27.0 + - + +
183E LYS* 6.2 0.4 - - + -
193E LEU* 4.6 6.1 - - + +
194E SER* 1.3 74.9 - - - +
196E SER* 1.3 60.4 + - - +
200E ALA 4.0 2.9 - - - -
201E LEU* 3.4 23.8 - - + +
225E VAL* 3.3 44.4 - - + +
226E LEU 4.0 3.4 - - - +
227E SER 3.8 12.1 - - - +
228E ALA* 3.4 18.8 - - + -
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Residues in contact with SER 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E HIS* 3.1 32.0 - - - -
177E ASN 3.4 10.7 + - - -
178E ALA 2.9 14.3 + - - -
179E ILE* 4.6 0.7 - - - -
180E ASN* 4.2 0.2 - - - -
195E VAL* 1.3 77.8 - - - +
197E LYS* 1.3 69.2 + - - +
198E ASP* 2.9 26.3 + - - +
199E HIS 3.3 7.6 + - - -
200E ALA 2.9 11.1 + - - +
225E VAL* 3.0 28.1 + - - +
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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
------------------------------------------------------------
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