Contacts of the strand formed by residues 445 - 448 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260K MET* 3.1 3.8 - - - -
261K GLY 2.8 30.7 + - - +
263K GLY* 3.3 10.9 + - - -
264K GLN* 2.8 49.7 + - + +
265K ASP* 3.0 26.2 + - - +
437K LEU* 3.9 6.8 - - + +
438K LEU 3.8 3.8 - - - +
439K ASN* 3.5 17.7 - - - +
440K MSE 3.7 5.0 - - - -
441K HIS* 3.1 23.1 + - - -
442K ALA 3.5 18.2 - - - +
444K TRP* 1.3 72.6 - - - +
446K ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLY 6.1 0.7 - - - -
174B VAL 6.5 0.7 - - - -
175B SER* 6.0 1.8 - - - -
200B ASN* 4.6 1.6 - - - +
252K TYR* 3.6 38.4 - - + +
258K MET* 3.6 39.0 - - + -
259K VAL 3.2 5.2 - - - +
260K MET* 4.0 20.6 - - + -
264K GLN* 4.2 0.2 - - - -
363K LEU* 5.1 2.1 - - + +
437K LEU* 3.1 12.0 - - - +
438K LEU* 3.1 54.0 + - + +
439K ASN* 4.4 10.5 - - - +
445K GLU* 1.3 81.5 - - - +
447K SER* 1.3 66.3 + - - +
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Residues in contact with SER 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ASN* 5.2 0.3 + - - -
258K MET* 2.9 10.4 - - - +
259K VAL* 2.8 38.0 + - - +
264K GLN* 2.8 34.8 + - - -
268K ILE* 3.8 15.8 - - - +
363K LEU* 4.3 3.1 - - - -
435K VAL* 4.9 2.0 - - - -
436K ALA 4.4 4.5 - - - -
437K LEU* 3.5 11.4 - - - -
446K ILE* 1.3 77.0 - - - +
448K SER* 1.3 61.1 + - - +
449K LYS 3.7 0.2 + - - -
452K ILE* 4.0 5.7 - - - +
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Residues in contact with SER 448 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ILE* 4.4 3.1 - - - +
13K TRP* 4.2 6.1 + - - -
257K SER 3.8 7.1 + - - -
258K MET* 4.3 1.6 - - - -
363K LEU* 3.4 21.6 - - - +
364K GLY* 3.8 7.6 - - - -
435K VAL* 5.1 0.2 - - - +
436K ALA 4.7 2.6 + - - -
447K SER* 1.3 73.4 - - - +
449K LYS* 1.3 66.7 + - - +
450K ALA* 3.5 15.9 + - - +
451K ASP* 2.8 42.0 + - - +
452K ILE* 2.9 15.1 + - - +
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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