Contacts of the strand formed by residues 237 - 241 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D PRO* 3.0 24.7 + - - +
97D SER* 3.2 25.7 - - - +
98D GLY 4.1 0.2 - - - -
101D ALA* 4.3 0.7 - - - -
225D THR 3.5 6.7 - - - -
227D THR* 4.6 0.6 - - - +
236D GLY* 1.3 75.0 - - - -
238D LEU* 1.3 66.6 + - - +
272D LYS* 2.8 21.8 + - - -
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 4.4 19.5 - - + -
86D PHE* 4.9 8.5 - - + -
92D ASN 3.2 21.3 - - - +
93D VAL* 3.4 30.3 - - + -
95D PRO* 4.6 0.7 - - - -
101D ALA* 4.0 4.8 - - - +
224D THR* 3.2 8.3 - - - -
225D THR* 2.8 54.0 + - + +
227D THR* 4.3 18.4 - - + -
231D LEU* 5.2 0.9 - - + -
237D GLY* 1.3 74.6 - - - +
239D ILE* 1.3 66.2 + - - +
240D LEU* 4.2 15.4 - - + +
272D LYS* 5.6 1.1 - - + -
276D LEU* 4.8 9.9 - - + -
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR* 4.1 15.5 - - + +
91D ALA* 3.1 5.8 - - - -
92D ASN* 2.8 43.5 + - + -
95D PRO* 4.0 12.8 - - + -
101D ALA* 4.2 11.2 - - + +
104D ALA* 4.1 14.6 - - + -
105D VAL* 4.6 2.5 - - + -
222D VAL* 3.8 21.5 - - + -
223D VAL 3.5 8.5 - - - +
224D THR* 4.3 6.7 - - + -
238D LEU* 1.3 79.2 - - - +
240D LEU* 1.3 67.9 + - - +
252D LEU* 4.3 13.5 - - + +
256D VAL* 3.5 32.8 - - + -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 4.2 18.2 - - + +
86D PHE* 3.6 33.4 - - + -
88D ALA* 4.3 9.4 - - + -
90D TYR* 3.4 7.2 - - - +
91D ALA* 3.8 19.5 - - + -
201D MET* 3.7 22.4 - - + -
217D VAL* 4.5 6.5 - - + -
222D VAL* 3.8 2.9 - - - +
223D VAL* 2.7 47.3 + - + +
225D THR* 4.6 8.1 - - + -
238D LEU* 4.2 15.9 - - + -
239D ILE* 1.3 83.7 - - - +
241D ALA* 1.3 64.7 - - - +
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Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ALA* 3.1 6.0 - - - +
89D ASP* 3.0 27.4 + - - +
90D TYR* 3.1 20.4 + - + -
217D VAL* 4.6 3.8 - - - -
220D ALA 5.7 0.4 - - - -
221D HIS 3.8 18.8 - - - +
222D VAL* 4.6 2.0 - - - +
223D VAL* 5.7 1.6 - - - -
240D LEU* 1.3 77.5 - - - +
242D LYS* 1.3 61.7 + - - +
244D GLY 5.7 0.2 - - - +
249D TYR* 3.6 26.5 - - + -
252D LEU* 4.8 6.1 - - + -
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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
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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