Contacts of the strand formed by residues 409 - 421 (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 ILE 409 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354K LEU* 4.5 15.0 - - + -
386K LEU 3.9 0.3 - - - +
387K ASN* 2.8 22.9 + - - +
388K MET* 3.0 45.5 + - + +
389K LYS* 3.7 5.2 - - + +
392K CYS* 5.0 5.4 - - - -
407K PRO* 3.7 3.6 + - + +
408K ASP* 1.3 75.1 + - - +
410K ILE* 1.3 61.5 + - - +
411K TYR* 4.7 5.8 - - + -
467K ILE* 3.7 26.0 - - + -
469K GLN 3.5 17.7 - - - +
470K VAL* 3.8 19.1 - - + -
58N PHE* 3.9 13.2 - - + -
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Residues in contact with ILE 410 (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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385K TYR* 3.6 22.7 - - + +
386K LEU 3.4 34.3 - - - +
387K ASN* 3.9 5.8 - - + +
408K ASP* 4.6 6.7 - - - +
409K ILE* 1.3 76.9 - - - +
411K TYR* 1.3 78.7 + - - +
468K ARG* 3.7 12.7 + - + +
469K GLN* 3.3 41.6 + - + +
471K ASN* 5.8 4.0 - - - +
31L ALA* 6.3 2.7 - - - -
34L LEU* 4.3 16.4 - - + -
35L GLN* 4.2 22.2 - - + +
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Residues in contact with TYR 411 (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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354K LEU* 3.3 27.5 - - + +
355K PRO* 3.1 22.8 + - - +
356K SER 4.5 3.1 - - - -
358K LEU* 3.6 37.7 - - + +
385K TYR* 3.4 29.1 - - - -
386K LEU* 2.8 18.6 + - + +
388K MET* 3.9 23.1 - - + -
409K ILE* 4.7 6.1 - - + -
410K ILE* 1.3 85.5 - - - +
412K GLU* 1.3 61.4 + - - +
465K TYR* 3.8 24.5 - + + -
466K THR 3.2 17.0 - - - +
467K ILE* 3.8 28.7 - - + -
468K ARG* 4.5 2.7 - - - -
58N PHE* 4.6 1.4 - - - -
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Residues in contact with GLU 412 (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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384K THR* 3.6 6.1 - - - +
385K TYR* 4.1 20.2 + - + -
411K TYR* 1.3 77.5 - - - +
413K LEU* 1.3 72.0 + - - +
414K ILE* 3.5 11.4 + - + +
433K LYS* 3.0 25.4 + - - +
465K TYR* 3.3 6.4 - - - -
466K THR* 3.2 35.8 + - + +
468K ARG* 3.2 42.8 + - + -
68N PRO* 5.8 2.8 - - - +
69N LEU* 4.4 14.6 - - - +
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Residues in contact with LEU 413 (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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382K PHE* 3.7 34.8 - - + -
383K PRO 4.6 2.7 - - - +
384K THR* 3.0 21.6 + - + +
412K GLU* 1.3 72.0 - - - +
414K ILE* 1.3 59.6 + - - +
415K GLY 3.3 20.6 - - - +
416K ILE* 3.7 19.3 - - + -
433K LYS* 3.2 25.3 + - - -
439K TRP* 4.1 16.3 - - + -
455K VAL* 6.2 0.2 - - + -
456K LEU* 4.7 9.2 - - + -
464K PHE 3.3 19.5 - - - +
465K TYR* 3.6 32.5 - - + +
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Residues in contact with ILE 414 (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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158K ASN* 4.9 11.9 - - - +
159K PRO* 5.2 9.6 - - + -
357K VAL* 4.7 8.3 - - + -
412K GLU* 3.8 9.6 - - + +
413K LEU* 1.3 79.5 - - - +
415K GLY* 1.3 62.3 + - - +
432K CYS* 3.8 7.8 - - - -
433K LYS* 3.2 31.9 + - - +
439K TRP* 4.1 8.3 - - - -
464K PHE* 2.9 22.0 + - + +
466K THR* 3.7 41.5 - - + +
69N LEU* 4.4 25.8 - - + -
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Residues in contact with GLY 415 (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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154K CYS* 5.7 2.5 - - - -
413K LEU* 3.3 10.4 - - - +
414K ILE* 1.3 85.1 - - - +
416K ILE* 1.3 64.3 + - - +
431K PHE 3.6 6.1 - - - -
432K CYS* 4.5 3.4 - - - -
439K TRP* 4.7 0.9 - - - -
463K LEU* 3.6 1.4 - - - -
464K PHE* 3.1 44.9 + - - -
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Residues in contact with ILE 416 (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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382K PHE* 3.9 15.5 - - + -
413K LEU* 3.7 33.0 - - + -
415K GLY* 1.3 81.3 - - - +
417K VAL* 1.3 67.3 + - - +
418K SER* 4.6 2.5 - - - +
430K ALA* 3.5 1.2 - - - +
431K PHE* 2.5 68.2 + - + +
439K TRP* 4.8 6.5 - - + -
455K VAL* 4.9 13.2 - - + +
458K GLU* 5.6 2.2 - - + -
460K ALA* 3.9 20.9 - - + -
462K LEU 3.6 2.7 - - - +
463K LEU* 3.8 21.8 - - + -
464K PHE* 4.6 0.4 - - - -
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Residues in contact with VAL 417 (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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150K SER* 4.2 24.5 - - - +
151K ILE* 5.2 6.3 - - + -
154K CYS* 5.3 1.8 - - + -
238K ALA* 5.5 0.7 - - + -
416K ILE* 1.3 76.4 - - - +
418K SER* 1.3 56.6 + - - +
428K TYR* 4.5 18.4 - - + -
429K ILE 4.1 4.5 - - - +
430K ALA* 4.2 12.8 - - + +
460K ALA* 3.6 0.5 - - - -
461K TYR* 2.6 38.6 + - + +
462K LEU* 3.0 43.3 + - + -
464K PHE* 4.2 20.6 - - + -
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Residues in contact with SER 418 (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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416K ILE* 4.1 2.2 - - - -
417K VAL* 1.3 74.9 - - - +
419K HIS* 1.3 59.2 + - - +
427K HIS 4.1 0.2 - - - +
428K TYR* 3.6 4.8 - - - -
429K ILE* 2.6 69.3 + - - +
431K PHE* 4.1 17.9 - - - -
458K GLU* 4.7 8.8 + - - -
459K GLN 3.3 23.3 - - - -
460K ALA* 4.7 0.9 - - - -
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Residues in contact with HIS 419 (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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375K LYS* 3.1 36.0 + - - +
417K VAL 4.3 1.0 + - - -
418K SER* 1.3 75.4 - - - +
420K LYS* 1.3 60.1 + - - +
421K GLY 3.9 10.3 - - - -
422K THR 3.5 24.7 - - - -
426K GLY* 3.5 12.1 - - - -
427K HIS 3.3 20.0 - - - -
428K TYR* 3.3 41.5 - + + -
459K GLN* 3.7 21.1 + - - +
461K TYR* 4.3 10.3 - - + +
73O LEU* 3.5 26.7 - - + +
74O ARG 3.3 17.4 + - - -
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Residues in contact with LYS 420 (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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120D SER* 4.7 15.6 + - - +
375K LYS* 3.6 2.9 - - - +
419K HIS* 1.3 77.6 - - - +
421K GLY* 1.3 61.6 + - - +
426K GLY* 3.2 1.0 - - - -
427K HIS* 2.8 38.9 + - + +
459K GLN* 5.1 2.9 - - - +
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Residues in contact with GLY 421 (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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375K LYS* 3.2 24.4 + - - +
377K ASP* 4.7 4.2 - - - +
419K HIS* 3.9 0.6 - - - -
420K LYS* 1.3 80.2 - - - +
422K THR* 1.3 68.2 + - - +
425K GLU* 3.3 11.7 - - - -
426K GLY* 3.7 3.1 - - - -
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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