Contacts of the strand formed by residues 438 - 442 (chain K) in PDB entry 6T9L
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 GLN 438 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433K LYS* 4.1 0.7 - - - -
434K ILE* 3.3 36.1 + - + +
435K SER 5.0 1.6 - - - +
436K GLY* 4.4 4.5 - - - +
437K GLY* 1.3 77.8 - - - +
439K TRP* 1.3 77.1 + - - +
440K PHE* 3.6 27.8 - - + -
449K SER* 3.5 20.6 + - - -
450K ILE 3.8 12.1 + - - +
451K SER* 5.7 0.2 - - - +
48M TYR* 6.3 0.2 - - + -
50M PHE* 5.9 1.0 - - - -
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Residues in contact with TRP 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K THR* 5.7 4.3 - - + -
413K LEU* 4.1 28.3 - - + -
414K ILE 4.1 14.4 - - - -
415K GLY* 4.3 0.7 - - - -
416K ILE* 4.7 5.2 - - + -
431K PHE* 3.7 18.6 - - + -
432K CYS* 3.5 24.5 - - - -
433K LYS* 3.4 50.2 - - + +
437K GLY 3.9 6.9 + - - -
438K GLN* 1.3 92.7 + - - +
440K PHE* 1.3 70.9 + - - +
449K SER* 3.7 0.3 - - - -
450K ILE* 3.4 31.4 + - + +
451K SER 4.4 0.7 - - - +
452K GLN* 3.4 44.3 - - + +
455K VAL* 4.1 26.2 - - + -
456K LEU* 5.9 0.9 - - + -
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Residues in contact with PHE 440 (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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136K LEU* 3.9 27.4 - - + -
431K PHE* 3.5 14.9 - - - +
432K CYS 3.3 22.5 + - - +
434K ILE* 3.6 38.6 - - + -
438K GLN* 3.6 29.4 - - + -
439K TRP* 1.3 84.5 - - - +
441K LYS* 1.3 60.7 + - - +
442K PHE* 3.7 24.6 + + + -
447K VAL* 5.5 0.9 - - + -
448K SER 3.3 11.0 - - - +
449K SER* 3.6 29.6 - - - +
450K ILE* 3.9 7.5 - - - +
48M TYR* 4.5 17.0 - + - -
58M ILE* 4.1 14.4 - - + -
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Residues in contact with LYS 441 (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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429K ILE* 4.6 23.3 - - + +
431K PHE* 3.6 28.3 - - + -
440K PHE* 1.3 70.9 - - - +
442K PHE* 1.3 60.1 + - - +
443K ASN* 4.5 19.1 - - - +
446K MET* 3.1 23.5 - - + +
447K VAL* 3.5 2.4 - - - -
448K SER* 2.5 40.4 + - - +
449K SER 4.9 0.2 - - - +
450K ILE* 4.2 13.6 - - + +
54M GLY* 5.0 10.7 + - - -
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Residues in contact with PHE 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K LEU* 3.8 19.3 - - + -
137K SER 5.9 0.7 - - - -
150K SER* 5.6 2.4 - - - -
153K GLN* 3.4 38.1 - - + +
157K HIS* 3.3 40.4 - + - -
428K TYR 5.4 0.2 - - - +
429K ILE* 4.3 2.9 - - - -
430K ALA* 3.0 45.0 + - + +
431K PHE 5.2 0.2 - - - -
432K CYS* 3.6 31.6 - - + -
434K ILE* 5.2 1.3 - - + -
440K PHE* 3.7 21.3 + + + -
441K LYS* 1.3 75.0 - - - +
443K ASN* 1.3 63.6 + - - +
446K MET 4.4 0.4 - - - -
447K VAL* 4.1 22.2 - - + -
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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