Contacts of the strand formed by residues 460 - 470 (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 ALA 460 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362K LEU* 3.5 10.0 - - + +
364K ARG* 2.7 37.7 + - - +
382K PHE* 4.2 19.3 - - + -
416K ILE* 3.9 37.7 - - + -
417K VAL 3.8 4.7 - - - +
458K GLU 3.0 6.2 + - - +
459K GLN* 1.3 70.1 - - - +
461K TYR* 1.3 55.5 + - - +
462K LEU 4.6 0.4 - - - +
463K LEU* 4.5 10.5 - - + -
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Residues in contact with TYR 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237K ASP* 3.6 17.2 + - - -
238K ALA* 5.0 0.4 - - + -
239K HIS* 3.8 15.5 - - + +
360K LEU 4.2 0.2 - - - +
361K GLN* 3.2 26.0 + - + -
362K LEU* 3.4 44.0 + - - +
364K ARG* 4.1 18.8 - - + +
365K PHE* 4.9 8.7 - + - -
417K VAL* 2.6 18.8 + - + +
419K HIS* 4.3 16.2 - - + +
428K TYR* 4.5 17.3 - + - -
459K GLN 3.6 1.4 + - - +
460K ALA* 1.3 74.1 - - - +
462K LEU* 1.3 87.1 + - + +
463K LEU* 4.7 2.0 - - - -
71O LEU 5.2 1.9 + - - -
73O LEU* 3.7 30.9 - - + +
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Residues in contact with LEU 462 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE* 4.6 17.7 - - + -
238K ALA* 5.3 0.9 - - + -
239K HIS* 4.5 20.9 - - + +
242K TRP* 5.5 6.7 - - + -
359K VAL* 5.1 6.7 - - + -
360K LEU 3.7 9.4 - - - +
361K GLN* 3.9 26.0 - - + -
415K GLY 4.6 0.4 - - - -
416K ILE* 3.6 7.3 - - - +
417K VAL* 3.0 52.4 + - + +
461K TYR* 1.3 105.3 + - + +
463K LEU* 1.3 67.3 + - - +
464K PHE* 5.0 13.2 - - + -
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Residues in contact with LEU 463 (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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316K LEU* 4.0 18.4 - - + -
359K VAL* 3.4 4.2 - - - +
360K LEU* 3.1 45.3 + - + +
362K LEU* 4.1 30.1 - - + -
382K PHE* 4.2 14.1 - - + -
413K LEU* 4.4 0.4 - - + -
415K GLY 3.6 3.6 - - - -
416K ILE* 3.8 17.7 - - + -
460K ALA* 4.5 5.8 - - + -
462K LEU* 1.3 87.1 - - - +
464K PHE* 1.3 72.8 + - - +
465K TYR* 3.6 37.5 - - + +
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Residues in contact with PHE 464 (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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151K ILE* 6.1 1.8 - - + -
154K CYS* 3.5 40.6 - - + -
242K TRP* 5.0 21.8 - + - -
279K PHE* 6.3 2.2 - + - -
357K VAL* 5.2 9.4 - - + -
358K LEU 3.8 1.1 - - - -
359K VAL* 3.6 28.3 - - + -
413K LEU* 3.3 7.3 - - - +
414K ILE* 2.9 40.2 + - + -
415K GLY* 3.1 37.8 + - - +
417K VAL* 4.2 19.7 - - + -
462K LEU* 5.0 11.7 - - + -
463K LEU* 1.3 82.4 - - - +
465K TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 465 (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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316K LEU* 3.6 23.8 - - + +
356K SER 4.1 0.3 - - - +
357K VAL* 3.3 4.7 - - - +
358K LEU* 2.4 53.3 + - + +
360K LEU* 4.7 11.9 - - + -
382K PHE* 4.1 4.2 - - - +
383K PRO* 3.0 23.6 + - - +
384K THR 4.2 2.9 - - - -
386K LEU* 3.8 22.2 - - + -
411K TYR* 3.8 31.0 - - + -
412K GLU 3.3 7.4 - - - -
413K LEU* 3.6 38.7 - - + +
463K LEU* 3.6 34.4 - - + +
464K PHE* 1.3 74.6 - - - +
466K THR* 1.3 58.5 + - - +
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Residues in contact with THR 466 (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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159K PRO* 5.8 3.3 - - + +
160K TYR* 4.2 8.1 + - - -
356K SER 3.5 8.8 + - - -
357K VAL* 4.0 14.2 - - - +
411K TYR* 3.2 16.4 - - - -
412K GLU* 3.2 27.9 + - + +
414K ILE* 3.7 39.7 - - + -
464K PHE 4.2 0.8 - - - -
465K TYR* 1.3 72.9 - - - +
467K ILE* 1.3 83.4 + - - +
468K ARG 3.5 0.2 + - - -
68N PRO* 5.1 15.2 - - + +
69N LEU* 5.5 1.3 - - + -
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Residues in contact with ILE 467 (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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160K TYR* 3.3 26.0 - - - +
355K PRO 5.6 0.7 - - - +
356K SER* 2.8 23.1 + - - +
409K ILE* 3.7 18.6 - - + -
410K ILE 4.5 0.2 - - - +
411K TYR* 3.8 12.3 - - + -
466K THR* 1.3 87.7 + - - +
468K ARG* 1.3 64.2 + - - +
469K GLN 4.6 1.3 - - - +
49N MET* 3.9 24.2 - - + -
58N PHE* 3.7 34.5 - - + -
64N LEU* 4.3 17.7 - - + -
65N ILE 4.7 8.1 - - - +
68N PRO* 4.7 12.6 - - - +
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Residues in contact with ARG 468 (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* 4.1 7.7 + - + -
410K ILE* 3.7 15.4 + - + +
411K TYR 4.5 2.2 - - - -
412K GLU* 3.2 46.9 + - + +
466K THR 3.5 1.4 + - - -
467K ILE* 1.3 76.6 - - - +
469K GLN* 1.3 63.4 + - + +
34L LEU* 3.7 48.8 - - + +
39L VAL* 4.9 11.3 - - - +
43L LYS* 5.3 4.6 - - - +
48N HIS* 3.4 23.2 + - - -
49N MET* 3.8 8.4 - - - +
66N GLU* 5.0 0.9 - - - +
67N ASP* 3.6 45.5 + - - +
68N PRO* 5.6 2.0 - - - -
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Residues in contact with GLN 469 (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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408K ASP 4.3 0.5 - - - +
409K ILE* 3.5 6.4 - - - +
410K ILE* 3.3 38.5 + - + +
467K ILE* 4.6 0.4 - - - +
468K ARG* 1.3 84.9 - - + +
470K VAL* 1.3 63.0 + - - +
471K ASN* 2.8 31.4 + - - +
27L ASN* 4.0 6.6 + - - -
30L LYS* 3.8 32.7 - - - +
31L ALA* 5.0 1.5 - - - -
34L LEU* 4.1 16.2 - - + +
48N HIS* 3.3 39.2 + - + +
49N MET* 3.7 8.9 - - - +
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Residues in contact with VAL 470 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407K PRO* 5.1 3.4 - - + -
408K ASP 3.8 5.8 - - - +
409K ILE* 3.8 20.4 - - + -
469K GLN* 1.3 73.8 - - - +
471K ASN* 1.3 73.8 + - - +
27L ASN* 5.3 0.9 - - - +
48N HIS 3.0 18.4 + - - +
49N MET* 3.7 34.1 - - + -
50N ASN* 3.6 18.1 + - - +
53N SER* 3.7 23.6 - - - +
54N LEU* 4.7 3.4 - - + -
57N TYR* 6.2 0.4 - - + -
58N PHE* 4.5 16.4 - - + -
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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