Contacts of the helix formed by residues 445 - 455 (chain K) in PDB entry 6R1U
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 ASN 445 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269K PHE* 5.6 0.5 - - - -
439K VAL* 4.0 15.4 - - + +
440K ASN 4.1 6.3 + - - +
441K GLY 2.9 24.2 + - - +
442K CYS* 3.0 19.1 + - - +
443K ILE 3.0 2.0 - - - -
444K ASN* 1.3 77.4 - - - +
446K PRO* 1.3 72.7 - - - +
447K VAL* 2.9 24.1 + - - +
448K ALA* 2.9 18.2 + - - +
449K LEU* 3.1 10.6 + - - +
568K PHE* 3.6 12.2 - - - -
806K THR* 2.6 36.2 + - - +
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Residues in contact with PRO 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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282K LEU* 4.0 4.0 - - + -
444K ASN 3.5 8.0 - - - +
445K ASN* 1.3 93.6 - - - +
447K VAL* 1.3 56.5 + - + +
449K LEU* 3.2 14.8 + - + +
450K MET* 2.9 35.9 + - + +
568K PHE* 3.9 7.6 - - + -
806K THR* 3.8 11.2 - - + -
809K TYR* 3.6 28.3 - - + -
810K LEU* 3.5 34.1 - - + -
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Residues in contact with VAL 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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439K VAL* 3.7 30.3 - - + -
445K ASN* 2.9 8.9 + - - +
446K PRO* 1.3 77.0 - - + +
448K ALA* 1.3 59.4 + - - +
450K MET* 3.3 16.3 + - + +
451K CYS* 2.9 32.7 + - - -
458K MET* 4.8 0.4 - - - -
575K LEU* 4.1 4.9 - - + -
579K TYR* 3.9 24.5 - - + +
582K ILE* 3.9 17.3 - - + -
805K VAL* 4.8 3.6 - - + -
806K THR* 3.2 29.6 - - - +
809K TYR* 6.1 0.9 - - + -
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Residues in contact with ALA 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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266K ASN* 4.4 5.2 + - - -
268K TYR* 3.9 28.2 - - + -
269K PHE* 4.5 3.8 - - + -
439K VAL* 5.2 0.6 - - - +
442K CYS* 3.3 28.7 - - + +
445K ASN* 2.9 8.1 + - + +
447K VAL* 1.3 75.2 - - - +
449K LEU* 1.3 66.5 + - - +
451K CYS* 3.3 3.6 + - - +
452K GLU* 3.1 21.7 + - - +
458K MET* 4.1 17.1 - - + +
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Residues in contact with LEU 449 (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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269K PHE* 3.8 23.6 - - + -
318K TRP* 4.1 17.7 - - + +
319K TYR* 4.8 7.0 - - + -
322K CYS* 3.5 35.4 - - + -
364K THR* 4.2 18.4 - - + -
365K GLY* 4.2 24.0 - - - -
445K ASN 3.1 9.8 + - - +
446K PRO* 3.4 17.0 - - + +
448K ALA* 1.3 77.8 - - - +
450K MET* 1.3 56.7 + - - +
452K GLU* 3.1 6.9 + - - +
453K GLN* 3.0 30.3 + - - +
809K TYR* 5.6 0.7 - - + +
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Residues in contact with MET 450 (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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365K GLY* 3.6 30.3 - - - -
366K VAL* 3.7 18.4 - - + +
446K PRO* 2.9 31.3 + - + +
447K VAL* 3.3 14.8 + - + +
449K LEU* 1.3 78.0 - - + +
451K CYS* 1.3 62.4 + - - +
453K GLN* 3.4 12.2 + - - +
454K LEU* 3.0 31.7 + - - +
582K ILE* 3.7 35.9 - - + -
586K LEU* 4.3 2.2 - - - -
805K VAL* 6.6 0.2 - - + -
809K TYR* 3.8 37.9 - - + -
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Residues in contact with CYS 451 (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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447K VAL* 2.9 25.4 + - - +
448K ALA* 3.7 7.2 - - - +
449K LEU 3.2 0.4 - - - -
450K MET* 1.3 73.2 - - - +
452K GLU* 1.3 61.8 + - - +
454K LEU* 3.2 2.0 + - - +
455K GLY 2.8 9.4 + - - -
456K ILE* 2.8 56.4 + - + +
458K MET* 3.9 22.4 - - + -
575K LEU* 3.6 30.5 - - - -
582K ILE* 4.5 6.3 - - - -
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Residues in contact with GLU 452 (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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266K ASN* 2.7 39.8 + - - +
269K PHE* 3.9 15.7 - - + -
322K CYS* 3.6 19.7 - - - -
323K LYS* 3.4 21.7 + - - -
448K ALA 3.1 11.2 + - - +
449K LEU 3.1 10.0 + - - +
451K CYS* 1.3 75.9 - - - +
453K GLN* 1.3 62.5 + - - +
454K LEU 3.2 0.7 + - - -
455K GLY* 3.2 11.9 + - - +
456K ILE 5.2 0.7 - - - -
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Residues in contact with GLN 453 (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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318K TRP* 3.6 11.7 - - - -
322K CYS* 2.9 38.3 + - - +
323K LYS* 4.0 24.3 - - + +
364K THR 3.0 23.2 + - - -
365K GLY* 3.6 0.5 - - - -
366K VAL* 2.8 39.9 + - + +
367K LEU* 3.9 7.5 - - - +
449K LEU* 3.0 20.9 + - - +
450K MET* 3.6 16.3 - - - +
451K CYS 3.3 0.2 - - - -
452K GLU* 1.3 77.8 - - - +
454K LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 454 (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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323K LYS* 5.9 0.2 - - - -
366K VAL* 4.0 15.9 - - + -
450K MET 3.0 21.9 + - - +
451K CYS 3.9 0.4 - - - +
453K GLN* 1.3 78.2 - - - +
455K GLY* 1.3 65.0 + - - +
456K ILE* 3.7 33.4 - - + +
581K VAL* 4.4 6.5 - - + +
582K ILE* 4.0 30.1 - - + -
585K LYS* 3.7 37.2 - - + -
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Residues in contact with GLY 455 (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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323K LYS* 5.3 5.5 - - - +
451K CYS 2.8 5.6 + - - -
452K GLU* 3.2 11.3 + - - -
453K GLN 3.4 0.2 - - - -
454K LEU* 1.3 80.5 - - - +
456K ILE* 1.3 59.9 + - - +
457K SER 4.2 0.5 + - - -
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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