Contacts of the strand formed by residues 124 - 128 (chain E) in PDB entry 3ECS
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 THR 124 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E GLY 4.7 2.4 + - - -
123E ALA* 1.3 72.2 + - - +
125E ILE* 1.3 62.1 + - - +
149E SER* 3.6 18.8 - - - +
151E TYR* 3.8 31.6 - - + -
189E LYS 3.4 24.8 + - - +
190E ALA* 3.7 4.5 - - - -
191E ASP* 2.7 43.7 + - - +
192E LEU* 3.5 5.8 + - - +
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Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ILE* 4.2 17.3 - - + -
123E ALA* 4.8 4.9 - - + -
124E THR* 1.3 79.9 - - - +
126E LEU* 1.3 67.5 + - - +
127E THR* 4.2 11.4 - - + -
138E LEU* 3.7 26.2 - - + -
148E PHE* 4.0 17.5 - - + -
149E SER 2.8 14.9 + - - +
150E VAL* 3.2 10.7 - - + +
151E TYR* 2.7 34.4 + - - +
190E ALA* 4.7 1.6 - - - -
192E LEU* 3.6 19.3 - - + +
194E ILE* 4.0 28.5 - - + -
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Residues in contact with LEU 126 (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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125E ILE* 1.3 73.9 - - - +
127E THR* 1.3 68.8 + - - +
151E TYR* 3.2 33.7 - - + +
152E VAL* 4.3 1.8 - - - +
153E THR* 5.0 2.2 - - + +
178E VAL* 5.3 3.1 - - + -
183E VAL* 4.4 5.2 - - + -
186E ILE* 4.4 18.4 - - + -
187E MSE 3.7 35.2 - - + -
190E ALA* 4.0 14.1 - - + -
192E LEU 3.0 13.6 + - - +
193E VAL* 3.2 14.3 - - + +
194E ILE 3.1 24.1 + - - -
215E MSE 3.7 23.8 - - + -
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Residues in contact with THR 127 (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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125E ILE* 4.2 14.3 - - + -
126E LEU* 1.3 76.9 - - - +
128E HIS* 1.3 62.9 + - - +
129E ALA 4.5 2.5 + - - -
134E VAL* 4.6 20.0 - - + -
138E LEU* 5.1 9.2 - - + -
150E VAL* 4.4 6.7 - - + +
151E TYR 2.9 8.1 + - - +
152E VAL* 3.3 38.2 - - - +
153E THR 3.5 3.6 + - - -
164E MSE 4.9 5.4 - - - +
168E LEU* 5.5 0.9 - - - +
194E ILE* 2.9 29.4 - - + +
195E VAL* 4.4 2.2 - - - -
215E MSE 3.7 12.9 - - - +
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Residues in contact with HIS 128 (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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181D ALA* 5.0 2.7 - - + -
127E THR* 1.3 77.2 - - - +
129E ALA* 1.3 73.1 + - + +
130E TYR 3.8 3.5 + - - +
131E SER* 5.3 3.3 - - - -
153E THR* 2.5 35.7 + - + +
155E SER* 3.8 19.7 + - - -
180E ASP* 4.3 8.1 - - + -
195E VAL* 4.0 18.3 - - + +
196E GLY 5.8 1.2 + - - -
208E ASN* 4.8 3.4 - - - +
209E LYS* 3.7 13.1 + - + +
210E ILE 2.9 27.2 + - - -
211E GLY* 3.6 14.7 + - - -
212E THR* 3.5 28.3 - - - +
215E MSE 3.9 16.9 - - + +
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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