Contacts of the strand formed by residues 135 - 140 (chain E) in PDB entry 3V62
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 SER 135 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TYR* 3.9 2.3 - - - +
134E ASP* 1.3 75.8 - - - +
136E THR* 1.3 68.4 + - - +
137E LEU 4.3 0.2 - - - -
162E ILE* 3.7 23.4 - - - +
197E LEU* 5.0 0.4 - - - -
198E GLU 3.4 7.4 - - - -
199E MET* 3.0 29.1 - - - +
201E GLN 3.1 11.6 + - - -
203E VAL* 3.4 16.4 - - - +
227E ILE 4.6 0.2 - - - -
228E ARG* 3.3 2.6 - - - -
229E LEU* 3.1 28.3 + - - +
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Residues in contact with THR 136 (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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133E TYR* 4.1 5.7 + - - +
135E SER* 1.3 79.0 + - - +
137E LEU* 1.3 63.7 + - - +
196E LYS 4.0 0.9 - - - +
197E LEU* 3.7 1.4 - - - -
198E GLU* 2.8 48.2 + - + +
226E GLY* 6.1 0.9 - - - -
227E ILE 3.3 5.6 - - - +
228E ARG* 3.2 46.3 + - + +
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E THR* 1.3 78.7 - - - +
138E SER* 1.3 58.7 + - - +
139E LEU* 3.7 23.3 - - + -
160E ILE* 5.6 1.8 - - + -
162E ILE* 4.1 25.8 - - + -
167E ILE* 3.9 35.7 - - + -
169E PHE* 4.8 2.9 - - + -
182E ILE* 4.4 8.3 - - + -
195E ILE* 5.1 0.9 - - + -
196E LYS 3.1 11.7 - - - +
197E LEU* 4.3 13.2 - - + -
225E VAL 4.0 0.2 - - - +
226E GLY* 3.5 1.9 - - - -
227E ILE* 2.7 69.7 + - + +
229E LEU* 4.4 1.8 - - + -
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Residues in contact with SER 138 (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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137E LEU* 1.3 74.8 - - - +
139E LEU* 1.3 67.6 + - - +
195E ILE* 3.5 3.6 - - - +
196E LYS* 2.9 40.3 + - - +
224E ARG* 3.0 8.4 + - - -
225E VAL 3.1 15.9 - - - -
226E GLY* 4.3 3.6 - - - -
303E SO4 2.8 37.8 + - - -
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Residues in contact with LEU 139 (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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137E LEU* 3.7 19.7 - - + -
138E SER* 1.3 81.0 - - - +
140E PRO* 1.4 81.6 - - + +
143E GLU* 4.8 4.5 - - + -
144E PHE* 4.1 26.5 - - + +
147E ILE* 4.7 7.9 - - + -
169E PHE* 5.1 2.0 - - + -
182E ILE* 4.2 14.8 - - + -
194E SER 3.6 0.9 - - - -
195E ILE* 3.7 24.9 - - + -
224E ARG* 3.2 12.0 - - - +
225E VAL* 3.0 44.3 + - + +
227E ILE* 3.8 13.9 - - + -
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Residues in contact with PRO 140 (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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139E LEU* 1.4 91.3 - - + +
141E SER* 1.3 64.8 + - - +
142E SER* 3.3 6.5 - - - +
143E GLU* 3.3 33.2 - - + +
144E PHE 3.2 16.6 + - - -
192E GLU 3.6 5.6 - - - +
193E THR* 3.4 37.7 - - + +
194E SER 3.4 14.8 - - - +
195E ILE* 4.9 0.9 - - + -
223E ASP 3.4 11.4 - - - +
224E ARG* 3.8 4.6 - - + +
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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