Contacts of the strand formed by residues 126 - 129 (chain E) in PDB entry 3EGC
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 GLY 126 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E VAL 4.2 0.8 + - - -
70E VAL* 3.5 4.9 - - - +
71E GLY 2.9 22.9 + - - -
124E VAL* 3.2 5.9 - - - +
125E ASP* 1.3 81.2 - - - +
127E LEU* 1.3 64.0 + - - -
147E PHE* 4.0 7.4 - - - -
148E PRO* 3.3 16.8 - - - -
311E LEU* 3.7 13.5 - - - -
315E ILE* 4.3 1.2 - - - +
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLY* 3.4 24.9 - - - +
73E ILE* 3.9 9.0 - - + -
116E VAL* 3.8 41.3 - - + +
119E PHE* 3.9 24.9 - - + -
124E VAL* 4.0 6.3 - - + -
126E GLY* 1.3 76.2 - - - +
128E ILE* 1.3 66.6 + - - +
129E LEU* 4.9 5.4 - - + +
139E LEU* 5.3 0.7 - - + -
147E PHE* 3.6 18.1 - - + -
148E PRO 3.0 6.5 + - - -
149E ILE* 3.3 23.1 - - + +
150E VAL 3.0 25.5 + - - +
311E LEU* 3.6 4.9 - - - +
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Residues in contact with ILE 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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70E VAL* 4.6 0.4 - - + -
71E GLY 2.9 11.3 + - - +
72E LEU* 3.5 20.7 - - + +
73E ILE* 2.9 28.2 + - - +
89E VAL* 3.7 15.5 - - + -
127E LEU* 1.3 72.5 - - - +
129E LEU* 1.3 61.9 + - - +
150E VAL* 3.3 9.6 - - + +
152E VAL* 4.2 27.1 - - + -
307E ALA* 4.0 7.2 - - + -
308E MET* 3.4 57.2 - - + +
311E LEU* 3.7 18.8 - - + +
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Residues in contact with LEU 129 (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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73E ILE* 3.5 31.4 - - + +
112E GLU* 3.7 33.9 - - + +
116E VAL* 5.1 2.9 - - + -
127E LEU* 3.9 7.1 - - + -
128E ILE* 1.3 74.7 - - - +
130E ALA* 1.3 60.2 + - - +
131E PRO* 3.3 10.2 - - + +
136E HIS* 4.7 0.2 - - + -
138E TYR* 5.0 0.4 - - - +
139E LEU* 4.0 32.3 - - + -
149E ILE* 4.5 11.0 - - + -
150E VAL 2.9 9.6 + - - +
151E ALA* 3.0 8.9 - - - -
152E VAL* 2.8 31.8 + - - -
156E LEU* 4.0 19.3 - - + -
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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