Contacts of the strand formed by residues 405 - 416 (chain B) in PDB entry 3K2H
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 LYS 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B SER* 6.0 1.1 - - - -
400B TYR* 3.5 1.0 - - - +
401B VAL* 3.4 8.1 - - - +
402B SER* 3.1 27.9 + - - +
403B ASP* 3.5 32.7 + - - +
404B ASN* 1.3 82.5 - - - +
406B LEU* 1.3 61.7 + - - +
407B SER* 3.9 1.6 + - - +
441B LEU* 4.4 0.8 - - - +
442B GLY* 3.3 6.3 - - - -
443B LEU 3.8 24.5 - - - +
444B GLY* 3.9 15.3 - - - +
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Residues in contact with LEU 406 (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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366B ILE* 3.8 23.1 - - + -
399B PHE* 3.9 20.2 - - + -
400B TYR 3.4 13.0 - - - +
401B VAL* 3.9 12.8 - - + -
405B LYS* 1.3 72.9 - - - +
407B SER* 1.3 63.8 + - - +
432B THR* 3.6 22.3 - - + +
435B VAL* 3.6 19.1 - - + -
436B ALA* 3.4 34.5 - - + +
441B LEU* 4.2 13.7 - - + +
442B GLY 2.9 13.2 + - - +
443B LEU* 4.1 0.9 - - - -
444B GLY* 2.7 26.0 + - - -
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 3.7 24.7 - - - +
399B PHE* 3.3 11.5 - - - -
400B TYR* 2.8 40.7 + - - +
405B LYS 3.9 1.2 + - - -
406B LEU* 1.3 74.6 - - - +
408B CYS* 1.3 61.5 + - - +
432B THR* 4.4 2.0 - - - -
444B GLY* 3.7 3.8 - - - -
445B GLU* 2.9 36.3 + - - +
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Residues in contact with CYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 3.7 4.7 - - - -
397B PHE* 4.0 26.5 - - - -
398B GLN 3.3 10.1 - - - -
399B PHE* 3.8 20.6 - - + -
407B SER* 1.3 75.0 - - - +
409B MET* 1.3 59.3 + - - +
428B TYR* 4.4 13.2 - - - -
431B LEU* 5.9 0.2 - - - -
432B THR* 3.2 25.8 - - + +
445B GLU 2.9 6.7 + - - +
446B PHE* 3.4 10.6 - - + -
447B VAL* 2.8 32.7 + - - +
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Residues in contact with MET 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 3.4 18.8 - - + -
258A GLY* 3.3 21.3 - - - -
259A TYR 4.8 0.2 - - - +
411A HIS* 3.6 27.5 - - + -
449A ASN* 4.9 2.0 - - - -
450A LEU 3.3 24.7 - - - +
451A ALA* 4.0 13.9 - - - -
260B GLN* 3.8 10.1 - - - +
397B PHE* 3.1 4.7 - - - +
398B GLN* 2.8 35.5 + - + +
408B CYS* 1.3 74.9 - - - +
410B MET* 1.3 62.8 + - - +
447B VAL* 3.1 23.6 - - + +
449B ASN* 3.3 25.8 - - - +
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A HIS* 5.8 0.4 - - - -
394B HIS* 3.3 30.3 - - + -
396B PHE 3.4 10.8 - - - +
397B PHE* 4.0 6.1 - - + -
409B MET* 1.3 79.2 - - - +
411B HIS* 1.3 76.3 + - - +
412B GLN* 3.6 12.8 - - - +
424B ASN* 4.1 4.0 - - + -
428B TYR* 3.8 39.3 - - + +
446B PHE* 3.8 19.2 - - + -
447B VAL 2.9 7.9 + - - +
448B HIS* 3.4 30.6 - - + +
449B ASN* 3.0 28.3 + - - +
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Residues in contact with HIS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 3.4 35.2 - + + -
398A GLN* 2.9 28.3 + - + -
409A MET* 3.6 38.1 - - + -
411A HIS* 4.4 21.8 - - + +
449A ASN* 4.2 8.7 + - - -
395B CYS* 3.1 29.7 + - - -
396B PHE* 2.8 26.2 + - + +
410B MET* 1.3 76.8 - - - +
412B GLN* 1.3 61.0 + - - +
413B ARG* 3.7 11.5 - - - -
449B ASN* 4.1 5.5 - - + +
451B ALA* 4.2 1.7 - - + +
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Residues in contact with GLN 412 (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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393B CYS 3.3 15.3 - - - +
394B HIS* 4.1 2.5 - - - +
410B MET* 3.6 10.2 - - - +
411B HIS* 1.3 74.0 - - - +
413B ARG* 1.3 63.2 + - - +
414B SER 3.2 17.3 + - - +
415B CYS* 3.3 20.5 - - - +
421B VAL* 4.1 4.0 - - - +
424B ASN* 2.8 35.3 + - - +
448B HIS* 2.8 30.5 + - - +
449B ASN 3.0 17.7 + - - +
451B ALA* 3.0 26.2 + - - +
512B UMP 3.0 25.0 + - - -
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Residues in contact with ARG 413 (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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373A ARG 2.8 36.6 + - - +
374A ARG* 3.5 13.7 - - - +
376A ILE* 3.7 13.0 - - + -
398A GLN* 2.9 46.9 + - - +
380B TRP* 3.5 21.6 - - - -
390B LEU* 4.8 0.6 - - - +
391B PRO* 2.9 23.6 + - - +
392B PRO 2.8 17.9 + - - +
393B CYS* 2.9 29.2 + - - +
395B CYS* 4.1 6.3 - - - -
411B HIS* 3.7 4.1 - - - +
412B GLN* 1.3 72.3 - - - +
414B SER* 1.3 66.0 + - - +
451B ALA* 4.0 0.4 - - - -
452B ASP* 3.1 16.6 + - - +
512B UMP 2.6 43.4 + - - -
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Residues in contact with SER 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 3.3 13.8 + - - -
393B CYS* 3.5 6.0 - - - +
412B GLN* 3.2 18.7 + - - +
413B ARG* 1.3 98.0 - - - +
415B CYS* 1.3 60.3 + - - +
452B ASP* 3.5 6.3 - - - -
454B HIS* 3.4 3.8 - - - -
512B UMP 2.5 55.2 + - - +
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Residues in contact with CYS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLN* 3.3 45.5 - - - +
414B SER* 1.3 72.0 - - - +
416B ASP* 1.3 61.0 + - - +
417B LEU* 3.1 7.8 + - + +
421B VAL* 3.5 17.9 - - + -
450B LEU* 3.7 29.4 - - + -
451B ALA 3.9 1.1 - - - -
452B ASP 2.9 17.8 + - - +
453B ALA* 3.8 6.2 - - + -
454B HIS* 3.2 27.1 + - - +
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Residues in contact with ASP 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B CYS* 1.3 68.0 - - - +
417B LEU* 1.3 59.7 + - - +
418B GLY 3.2 5.4 + - - -
419B LEU* 3.0 30.0 + - - +
420B GLY 2.9 20.8 + - - -
421B VAL* 3.0 8.8 + - - +
454B HIS* 3.9 9.2 - - - +
456B TYR* 3.3 23.4 + - - -
459B HIS* 3.7 12.0 + - - -
510B SER 5.3 0.7 + - - -
512B UMP 2.8 31.6 + - - +
513B LYA 2.9 30.8 + - - +
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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