Contacts of the strand formed by residues 405 - 416 (chain A) in PDB entry 3KJR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A SER* 5.7 2.0 - - - -
400A TYR* 3.6 1.0 - - - +
401A VAL* 3.4 7.5 - - - +
402A SER 3.0 27.8 + - - +
403A ASP* 3.5 34.8 + - - +
404A ASN* 1.3 81.0 - - - +
406A LEU* 1.3 61.3 + - - +
407A SER* 3.8 1.7 + - - -
441A LEU* 4.8 0.2 - - - -
442A GLY* 3.4 11.7 - - - -
443A LEU 3.4 27.6 - - - +
444A GLY* 3.9 7.6 - - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ILE* 4.1 9.4 - - + -
399A PHE* 4.0 26.2 - - + -
400A TYR 3.5 13.0 - - - +
401A VAL* 4.0 17.5 - - + +
405A LYS* 1.3 72.0 - - - +
407A SER* 1.3 63.9 + - - +
432A THR* 3.5 28.7 - - + +
435A VAL* 3.6 17.3 - - + -
436A ALA* 3.4 35.2 - - + +
441A LEU* 4.2 11.5 - - + +
442A GLY 3.0 15.1 + - - +
443A LEU* 3.9 0.9 - - - -
444A GLY* 2.8 23.8 + - - -
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 3.3 12.2 - - - +
400A TYR* 2.8 42.6 + - - +
405A LYS 3.8 1.8 + - - -
406A LEU* 1.3 72.5 - - - +
408A CYS* 1.3 61.6 + - - +
432A THR* 4.5 1.3 - - - -
444A GLY* 3.6 5.4 - - - -
445A GLU* 2.9 34.6 + - - +
257B PHE* 3.7 26.9 - - - +
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Residues in contact with CYS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A PHE* 4.1 24.2 - - - -
398A GLN 3.2 9.0 - - - -
399A PHE* 3.7 18.8 - - + -
407A SER* 1.3 75.6 - - - +
409A MET* 1.3 63.1 + - - +
428A TYR* 4.2 11.4 - - - -
431A LEU* 5.9 0.2 - - - -
432A THR* 3.2 26.5 - - + +
445A GLU 3.0 6.7 + - - +
446A PHE* 3.5 16.7 - - + -
447A VAL* 2.8 28.6 + - - +
257B PHE* 3.8 4.2 - - - -
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN* 3.8 11.2 - - - +
397A PHE* 3.1 3.8 - - - +
398A GLN* 2.8 36.0 + - + +
408A CYS* 1.3 73.9 - - - +
410A MET* 1.3 60.3 + - - +
447A VAL* 3.2 25.6 - - + +
449A ASN* 3.2 26.5 - - - +
257B PHE* 3.4 17.4 - - + -
258B GLY* 3.4 32.8 - - - -
259B TYR 4.6 0.2 - - - +
411B HIS* 3.8 24.4 - - + -
449B ASN* 4.7 3.4 - - - -
450B LEU 3.5 11.0 - - - +
451B ALA* 4.1 16.2 - - - -
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Residues in contact with MET 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A HIS* 3.4 26.5 - - + -
396A PHE 3.4 12.1 - - - +
397A PHE* 3.9 7.4 - - + -
409A MET* 1.3 78.5 - - - +
411A HIS* 1.3 75.7 + - - +
412A GLN* 3.6 9.9 - - - +
424A ASN* 4.1 4.5 - - + -
428A TYR* 3.9 37.5 - - + +
446A PHE* 3.8 18.5 - - + -
447A VAL 3.0 7.3 + - - -
448A HIS* 3.4 31.6 - - + +
449A ASN* 2.9 34.1 + - - +
411B HIS* 5.6 0.4 - - - -
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Residues in contact with HIS 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A CYS* 3.2 28.6 + - - -
396A PHE* 2.8 26.6 + - + +
410A MET* 1.3 75.7 - - - +
412A GLN* 1.3 62.5 + - - +
413A ARG 3.8 10.1 - - - -
449A ASN* 3.9 5.6 - - + +
451A ALA* 4.2 2.6 - - + +
396B PHE* 3.5 33.2 - + - -
398B GLN* 2.9 31.6 + - + -
409B MET* 3.8 36.9 - - + -
411B HIS* 4.5 20.5 + - + +
449B ASN* 4.4 8.1 + - - -
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A CYS* 3.4 18.7 - - - +
394A HIS* 4.2 1.8 - - - +
410A MET* 3.6 10.4 - - - +
411A HIS* 1.3 75.3 - - - +
413A ARG* 1.3 62.2 + - - +
414A SER 3.0 25.8 + - - +
415A CYS* 3.4 28.5 - - - +
416A ASP 4.5 1.8 - - - +
420A GLY* 5.2 1.0 - - - -
421A VAL* 4.3 3.0 - - - +
424A ASN* 3.1 36.9 + - - +
448A HIS* 2.8 30.8 + - - +
449A ASN 2.9 15.6 + - - +
450A LEU* 4.2 0.3 - - - +
451A ALA* 3.0 27.7 + - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A TRP* 3.6 20.7 - - - -
390A LEU* 3.8 7.5 - - - +
391A PRO* 2.7 39.6 + - - +
392A PRO 2.8 17.2 + - - +
393A CYS* 2.9 33.5 + - - +
395A CYS* 4.0 10.3 - - - -
411A HIS* 3.8 4.1 - - + -
412A GLN* 1.3 72.9 - - - +
414A SER* 1.3 67.3 + - - +
451A ALA* 4.0 0.4 - - - -
452A ASP* 3.2 18.5 + - - +
373B ARG* 2.9 46.1 + - - +
374B ARG* 3.8 9.6 - - - +
376B ILE* 3.8 6.5 - - + -
398B GLN* 3.1 43.6 + - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ARG* 5.8 0.3 + - - -
393A CYS* 3.6 23.0 - - - +
412A GLN* 3.0 18.0 + - - +
413A ARG* 1.3 101.4 - - - +
415A CYS* 1.3 60.4 + - - +
416A ASP 4.1 1.3 + - - -
452A ASP* 3.5 6.1 - - - -
454A HIS* 3.3 10.7 + - - -
373B ARG* 3.2 30.3 + - - -
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Residues in contact with CYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A GLN* 3.4 46.2 - - - +
414A SER* 1.3 75.9 + - - +
416A ASP* 1.3 60.2 + - - +
417A LEU* 3.0 4.4 + - + -
421A VAL* 3.6 20.4 - - + -
450A LEU* 3.7 24.5 - - + -
451A ALA 4.0 1.1 - - - -
452A ASP 2.8 18.0 + - - +
453A ALA* 3.7 8.5 - - + -
454A HIS* 2.9 31.7 + - - +
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Residues in contact with ASP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLN* 4.5 2.6 - - - +
414A SER 4.1 1.6 + - - -
415A CYS* 1.3 66.6 - - - +
417A LEU* 1.3 59.9 + - - +
418A GLY 3.3 4.5 + - - -
419A LEU* 3.1 28.4 + - - +
420A GLY* 2.8 41.7 + - - +
421A VAL* 3.0 9.9 + - - +
454A HIS* 3.7 13.7 + - - +
456A TYR* 3.5 34.9 + - + +
459A HIS* 3.8 8.5 + - - -
509A MET* 5.1 8.0 - - - +
510A SER 5.5 2.1 + - - +
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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