Contacts of the strand formed by residues 237 - 241 (chain C) in PDB entry 1EQB
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 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C VAL 4.3 0.2 - - - +
95C PRO* 3.0 25.6 + - - +
97C SER* 3.2 25.7 - - - +
98C GLY 4.2 0.2 - - - -
101C ALA* 4.3 0.9 - - - -
225C THR 3.5 6.5 - - - -
227C THR* 4.6 1.3 - - - +
236C GLY* 1.3 74.4 - - - -
238C LEU* 1.3 66.0 + - - +
272C LYS* 2.9 21.8 + - - -
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 4.4 20.0 - - + -
86C PHE* 4.9 8.7 - - + -
92C ASN 3.2 21.5 - - - +
93C VAL* 3.3 29.6 - - + -
95C PRO* 4.6 0.7 - - - -
101C ALA* 4.0 4.8 - - - +
224C THR* 3.2 8.0 - - - -
225C THR* 2.8 54.7 + - + +
227C THR* 4.3 17.5 - - + -
231C LEU* 5.2 0.9 - - + -
237C GLY* 1.3 75.5 - - - +
239C ILE* 1.3 67.1 + - - +
240C LEU* 4.2 15.0 - - + -
272C LYS* 5.5 1.6 - - + -
276C LEU* 4.7 10.1 - - + -
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 4.1 14.6 - - + +
91C ALA* 3.2 5.2 - - - -
92C ASN* 2.8 45.3 + - + +
95C PRO* 4.0 13.9 - - + -
101C ALA* 4.2 11.0 - - + +
104C ALA* 4.1 14.6 - - + -
105C VAL* 4.7 4.0 - - + -
222C VAL* 3.8 21.8 - - + -
223C VAL 3.5 9.0 - - - +
224C THR* 4.2 6.7 - - + -
238C LEU* 1.3 78.5 - - - +
240C LEU* 1.3 68.2 + - - +
252C LEU* 4.3 11.7 - - + +
256C VAL* 3.5 31.9 - - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 4.2 17.7 - - + +
86C PHE* 3.6 32.8 - - + -
88C ALA* 4.3 9.4 - - + -
90C TYR* 3.5 6.3 - - - +
91C ALA* 3.8 19.3 - - + -
201C MET* 3.7 22.9 - - + -
217C VAL* 4.5 6.3 - - + -
222C VAL* 3.8 3.1 - - - +
223C VAL* 2.7 44.3 + - + +
225C THR* 4.6 7.9 - - + -
238C LEU* 4.2 16.8 - - + -
239C ILE* 1.3 82.8 - - - +
241C ALA* 1.3 64.8 + - - +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA* 3.1 6.4 - - - +
89C ASP* 3.1 27.4 + - - +
90C TYR* 3.1 19.9 + - + -
217C VAL* 4.6 4.9 - - - +
221C HIS 3.8 18.2 - - - +
222C VAL* 4.6 2.2 - - - +
223C VAL* 5.7 1.3 - - - -
240C LEU* 1.3 78.3 - - - +
242C LYS* 1.3 62.0 + - - +
249C TYR* 3.6 26.9 - - + -
252C LEU* 4.7 6.5 - - + -
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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