Contacts of the strand formed by residues 445 - 448 (chain E) in PDB entry 2GLJ
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 GLU 445 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260E MET* 3.1 5.4 - - - -
261E GLY 2.9 28.7 + - - -
263E GLY* 3.3 11.4 + - - -
264E GLN* 2.8 45.6 + - + +
265E ASP* 3.0 24.9 + - - +
437E LEU* 3.9 7.5 - - + +
438E LEU 4.0 3.6 - - - +
439E ASN* 3.5 19.5 - - - +
440E MSE 3.6 4.6 - - - -
441E HIS* 3.0 23.6 + - - -
442E ALA 3.5 15.9 - - - +
444E TRP* 1.3 73.1 - - - +
446E ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 446 (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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252E TYR* 3.6 38.8 - - + +
258E MET* 3.6 38.1 - - + -
259E VAL 3.2 4.9 - - - +
260E MET* 4.1 21.3 - - + -
363E LEU* 5.1 1.8 - - + +
437E LEU* 3.1 18.5 - - - +
438E LEU* 3.1 47.5 + - + +
439E ASN* 4.5 10.5 - - - +
445E GLU* 1.3 80.9 - - - +
447E SER* 1.3 67.4 + - - +
173H GLY 6.1 0.7 - - - -
174H VAL 6.5 0.4 - - - -
175H SER* 5.9 2.5 - - - -
200H ASN* 4.6 1.1 - - - +
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Residues in contact with SER 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E MET* 2.9 11.4 - - - +
259E VAL* 2.8 37.1 + - - +
264E GLN* 2.8 33.4 + - - -
268E ILE* 3.8 16.5 - - - +
363E LEU* 4.3 3.1 - - - -
435E VAL* 4.9 2.0 - - - -
436E ALA 4.4 5.8 - - - -
437E LEU* 3.5 12.1 - - - -
446E ILE* 1.3 76.6 - - - +
448E SER* 1.3 60.5 + - - +
449E LYS 3.7 0.2 + - - -
452E ILE* 3.9 6.5 - - - +
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Residues in contact with SER 448 (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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13E TRP* 4.2 5.2 + - - -
257E SER 3.8 8.0 + - - -
258E MET* 4.3 1.1 - - - -
363E LEU* 3.4 22.8 - - - +
364E GLY* 3.8 7.7 - - - -
435E VAL* 5.1 0.2 - - - +
436E ALA 4.7 2.6 + - - -
447E SER* 1.3 72.4 - - - +
449E LYS* 1.3 66.0 + - - +
450E ALA* 3.4 16.6 + - - +
451E ASP* 2.8 42.5 + - - +
452E ILE* 2.8 15.1 + - - +
203H ILE* 4.5 3.4 - - - +
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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