Contacts of the strand formed by residues 438 - 448 (chain B) in PDB entry 1KCX
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 GLU 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B ASP* 3.8 5.9 - - - +
417B MET* 5.2 14.7 - - + +
418B LYS 3.5 5.6 - - - +
419B THR* 3.4 21.0 + - + +
436B GLY 3.3 7.7 + - - +
437B MET* 1.3 74.7 - - - +
439B CYS* 1.3 61.8 + - - +
440B HIS* 3.8 21.3 + - + +
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Residues in contact with CYS 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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363B THR* 3.3 37.0 - - + -
364B VAL* 4.8 0.2 - - - -
367B ASP* 3.4 21.1 - - + -
417B MET* 3.2 4.3 - - - +
418B LYS* 2.8 38.5 + - - +
420B ILE* 4.0 13.2 - - - -
437B MET* 3.7 35.2 - - - -
438B GLU* 1.3 73.7 - - - +
440B HIS* 1.3 63.0 + - - +
441B GLY 3.7 2.0 + - - +
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Residues in contact with HIS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TRP* 3.2 17.9 + - - -
367B ASP* 2.9 30.8 + - - +
371B ALA* 4.2 18.0 - - + +
414B PRO 3.0 19.0 - - - +
415B ASP* 5.5 1.1 - - - -
416B LYS 4.1 8.7 - - - +
417B MET* 4.3 16.8 - - + +
438B GLU* 3.8 20.4 + - + +
439B CYS* 1.3 77.1 - - - +
441B GLY* 1.3 56.5 + - - +
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B THR* 3.3 24.4 - - - +
366B TRP* 3.8 11.8 - - - -
412B TRP* 3.1 18.9 - - - -
413B ASP 3.4 14.4 - - - -
414B PRO 3.9 2.9 - - - -
416B LYS 3.3 9.6 + - - -
418B LYS* 5.7 0.2 - - - -
439B CYS 3.7 1.6 - - - -
440B HIS* 1.3 75.5 - - - +
442B SER* 1.3 59.7 + - - -
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Residues in contact with SER 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B THR* 4.2 6.3 - - - -
412B TRP* 3.6 9.6 - - - -
413B ASP* 3.0 30.6 + - - +
416B LYS* 2.9 36.6 + - - +
418B LYS* 4.4 19.2 - - - +
441B GLY* 1.3 75.1 - - - -
443B PRO* 1.3 76.4 + - - +
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Residues in contact with PRO 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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98B ALA 4.3 9.0 - - - +
99B GLY* 3.6 32.1 - - - +
100B GLY* 3.8 3.4 - - - +
363B THR* 4.4 6.1 - - - +
410B VAL* 4.0 7.0 - - + -
411B ILE 3.7 5.4 - - - +
412B TRP* 3.6 18.8 - - + -
416B LYS* 4.5 7.6 + - - -
442B SER* 1.3 97.5 + - - +
444B LEU* 1.3 61.4 + - - +
446B VAL* 4.0 23.1 - - + -
454B PHE* 3.9 13.2 - - + -
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Residues in contact with LEU 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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63B ARG* 3.6 46.2 - - + +
411B ILE* 2.7 25.4 + - + +
413B ASP* 4.2 20.0 - - + +
416B LYS* 4.4 20.2 - - - +
442B SER 3.8 0.4 + - - -
443B PRO* 1.3 74.3 - - - +
445B VAL* 1.3 68.5 + - + +
454B PHE* 3.8 14.9 - - - -
455B GLU* 3.9 9.2 - - - -
456B ASP* 4.2 7.6 + - - +
457B GLY 4.9 1.8 + - - +
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Residues in contact with VAL 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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58B ILE* 4.4 20.9 - - + -
409B VAL 4.7 0.2 - - - -
410B VAL* 3.2 5.9 - - - +
411B ILE* 2.8 53.2 + - + -
444B LEU* 1.3 92.8 - - + +
446B VAL* 1.3 70.6 + - - +
447B ILE* 4.1 24.0 - - + -
452B ILE* 4.4 7.0 - - + -
454B PHE* 3.2 13.9 - - - +
455B GLU* 4.4 10.8 - - + +
456B ASP 5.3 0.9 - - - +
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Residues in contact with VAL 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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97B LEU* 3.4 28.0 - - + +
100B GLY* 4.1 4.9 - - - +
102B THR* 4.0 23.1 - - + -
409B VAL 3.6 2.5 - - - -
410B VAL* 4.0 11.0 - - + -
443B PRO* 4.0 22.4 - - + -
445B VAL* 1.3 79.7 - - - +
447B ILE* 1.3 68.3 + - - +
452B ILE* 3.6 1.4 - - - +
453B VAL* 2.9 39.2 + - + -
454B PHE* 2.9 30.3 + - + +
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Residues in contact with ILE 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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17B LEU* 3.8 21.3 - - + -
19B ILE* 3.9 26.2 - - + -
37B LEU* 4.1 10.1 - - + -
58B ILE* 4.3 10.8 - - + -
102B THR* 3.7 7.0 - - - +
407B ALA 3.9 3.6 - - - +
408B ASP* 3.2 5.2 - - - -
409B VAL* 2.6 47.9 + - + +
411B ILE* 5.7 1.8 - - + -
445B VAL* 4.1 12.6 - - + -
446B VAL* 1.3 79.4 - - - +
448B SER* 1.3 59.0 + - - +
450B GLY* 3.4 39.7 - - - +
451B LYS 3.2 6.3 - - - +
452B ILE* 4.2 9.9 - - + -
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Residues in contact with SER 448 (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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97B LEU* 4.1 22.0 - - - -
102B THR* 4.6 6.9 + - - -
132B CYS 4.3 4.4 + - - -
133B CYS* 4.1 21.3 - - - +
134B ASP* 4.7 1.4 + - - -
408B ASP* 3.8 7.3 + - - -
446B VAL 4.3 0.2 - - - -
447B ILE* 1.3 73.0 - - - +
449B GLN* 1.3 81.6 + - - +
450B GLY 3.1 0.4 - - - -
451B LYS* 2.9 24.3 + - - +
453B VAL* 4.2 15.0 - - - +
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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