Contacts of the strand formed by residues 437 - 448 (chain B) in PDB entry 2R8K
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 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS* 5.2 12.5 - - + +
201A ILE* 4.3 7.0 - - + -
202A ASN* 3.3 35.4 - - - +
431B GLU* 3.8 9.4 - - - +
436B LYS* 1.3 74.6 - - - +
438B VAL* 1.3 61.6 + - - +
439B ILE* 4.3 7.9 - - + -
467B ASN* 4.2 18.4 - - + +
507B ASP 3.7 0.3 - - - +
508B ILE* 3.4 2.8 - - - -
509B ILE* 2.6 74.5 + - + +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B VAL* 5.7 0.2 - - + -
427B ILE* 3.7 15.2 - - + +
430B LEU* 4.6 7.2 - - + -
431B GLU* 3.1 31.4 + - + +
434B TYR* 4.1 27.8 - - + -
436B LYS 3.8 4.0 + - - +
437B ILE* 1.3 76.8 - - - +
439B ILE* 1.3 74.3 + - - +
469B GLN* 3.6 13.9 - - - +
506B PHE* 3.8 36.1 - - + -
507B ASP 4.1 2.2 - - - +
508B ILE* 4.1 16.8 - - + -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B ILE* 3.9 3.8 - - + +
438B VAL* 1.3 84.3 - - - +
440B PRO* 1.3 70.0 - - + +
441B ARG* 3.6 25.1 + - - +
463B TYR* 4.3 17.5 - - + -
467B ASN* 3.8 37.0 - - + +
469B GLN* 5.1 5.2 - - + +
507B ASP* 2.8 48.0 + - + +
509B ILE* 3.5 34.8 - - + -
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Residues in contact with PRO 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B ILE* 4.6 6.5 - - + -
438B VAL* 4.3 2.6 - - + +
439B ILE* 1.3 83.6 - - - +
441B ARG* 1.3 60.3 + - - +
442B THR 3.7 2.2 - - - +
443B VAL* 5.8 0.4 - - + -
461B VAL* 3.5 2.0 - - + +
463B TYR* 3.1 39.3 + - + +
469B GLN* 3.6 21.1 - - - +
473B LEU* 4.9 6.5 - - + -
503B ILE* 3.9 38.6 - - + -
504B THR 4.0 6.7 - - - +
505B ASN 3.5 7.2 - - - +
506B PHE* 4.2 13.2 - - + -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B ILE* 3.8 20.2 - - - +
440B PRO* 1.3 77.7 - - - +
442B THR* 1.3 58.3 + - - +
460B PRO* 3.3 8.6 - - + +
461B VAL* 2.8 43.0 + - - +
463B TYR* 5.0 9.4 - - - -
505B ASN* 2.8 23.7 + - + +
507B ASP* 2.9 48.4 + - + +
509B ILE* 5.1 3.6 - - - +
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Residues in contact with THR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B PRO* 3.7 1.8 - - - +
441B ARG* 1.3 81.2 - - - +
443B VAL* 1.3 77.6 + - - +
458B SER* 3.8 9.2 + - - -
459B GLY 3.1 15.1 + - - -
460B PRO* 4.1 3.6 - - - -
461B VAL 4.5 0.2 - - - +
503B ILE* 3.4 3.8 - - - +
504B THR* 3.1 52.5 + - - +
505B ASN* 3.1 29.4 - - + +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B PRO* 5.8 0.7 - - + -
442B THR* 1.3 82.8 + - - +
444B SER* 1.3 74.3 + - - +
445B ILE* 4.1 11.0 - - + -
458B SER* 3.3 5.0 + - - -
459B GLY 2.8 35.7 + - - +
461B VAL* 4.7 14.6 - - + -
463B TYR* 5.8 0.2 - - - +
473B LEU* 3.5 30.5 - - + -
476B VAL* 4.6 12.3 - - + -
477B GLY* 5.3 1.8 - - - -
480B PHE* 3.8 4.2 - - + -
501B MET* 3.9 22.7 - - + -
502B THR 3.2 11.7 - - - +
503B ILE* 3.8 11.0 - - + -
504B THR* 6.1 0.2 - - - -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B VAL* 1.3 81.5 - - - +
445B ILE* 1.3 64.3 + - - +
446B SER* 3.9 2.3 + - - -
456B ARG* 3.9 20.6 - - - +
457B LYS 3.3 9.2 + - - -
458B SER* 3.8 15.8 - - - -
500B SER 3.7 1.0 - - - +
501B MET* 3.5 3.5 - - - -
502B THR* 2.9 40.1 + - - -
504B THR* 6.0 1.6 - - - -
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 4.7 4.5 - - + -
443B VAL* 4.1 3.8 - - + -
444B SER* 1.3 73.0 - - - +
446B SER* 1.3 67.9 + - - +
447B LEU* 5.1 4.9 - - + +
455B TYR 4.2 0.2 - - - +
456B ARG* 3.2 6.5 - - - +
457B LYS 2.8 34.6 + - - +
477B GLY* 4.0 11.9 - - - +
480B PHE* 3.5 36.6 - - + -
481B VAL* 4.6 17.9 - - + +
484B LEU* 4.8 4.7 - - + +
499B LEU* 4.3 15.3 - - + -
500B SER 3.4 7.0 - - - +
501B MET* 3.6 45.8 - - + -
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Residues in contact with SER 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B SER* 3.9 2.8 + - - -
445B ILE* 1.3 74.0 - - - +
447B LEU* 1.3 77.4 + - - +
454B VAL* 4.4 6.8 - - - +
455B TYR 3.7 4.9 + - - -
456B ARG* 3.8 31.6 + - - +
498B LYS* 6.0 2.5 - - - +
499B LEU* 3.7 3.3 - - - +
500B SER* 3.0 44.6 + - - +
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B CYS* 5.4 0.2 - - - -
445B ILE* 5.1 5.2 - - + +
446B SER* 1.3 84.4 + - - +
448B LYS* 1.3 63.3 + - - +
449B THR* 4.3 7.9 - - + -
454B VAL* 3.5 6.4 - - - +
455B TYR* 3.1 56.4 + - + +
481B VAL* 5.1 9.4 - - + -
484B LEU* 4.9 7.4 - - + -
493B TYR* 3.5 21.8 - - + +
496B LEU* 4.2 16.4 - - + -
498B LYS* 2.8 23.3 - - - +
499B LEU* 4.1 18.6 - - + -
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 1.3 74.8 - - - +
449B THR* 1.3 54.2 + - - +
452B TYR* 3.5 36.4 - - + +
453B GLU 3.1 5.4 - - - +
454B VAL* 3.6 24.2 - - + -
496B LEU* 3.6 4.2 - - - +
497B THR* 2.6 45.0 + - - +
498B LYS* 3.0 40.5 + - + +
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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