Contacts of the strand formed by residues 407 - 416 (chain B) in PDB entry 1KF9
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 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B GLU* 3.4 13.1 + - - +
381B VAL* 2.9 48.3 + - + +
406B LYS* 1.3 76.9 - - - +
408B TYR* 1.3 65.0 + - - +
430B TYR* 3.2 27.8 - - - +
431B VAL 3.0 17.9 - - - +
432B THR* 3.4 22.4 - - + +
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Residues in contact with TYR 408 (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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378B TYR* 4.1 14.6 - + + -
379B LYS 3.5 6.3 - - - +
380B GLU* 3.3 33.4 - - + -
381B VAL 4.6 0.9 - - - -
387B LYS* 4.2 16.2 + - - -
401B SER 5.0 0.5 + - - -
402B LEU* 3.9 26.6 - - + +
403B LYS* 3.4 51.7 + - - +
406B LYS* 3.7 23.8 + - + +
407B GLU* 1.3 83.2 - - - +
409B GLU* 1.3 61.9 + - - +
410B VAL* 5.7 1.8 - - + -
430B TYR* 3.5 4.5 - - - -
431B VAL* 2.6 45.5 + - + +
433B LEU* 4.1 11.2 - - + -
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR* 3.2 3.8 - - - +
379B LYS* 3.0 60.2 + - + +
381B VAL* 3.4 19.0 - - + +
386B TRP* 3.5 28.0 - - + -
408B TYR* 1.3 74.7 - - - +
410B VAL* 1.3 63.4 + - - +
428B VAL* 4.3 14.2 - - + +
429B LEU 3.0 11.4 - - - +
430B TYR* 3.7 29.6 + - + -
431B VAL* 5.6 0.2 - - - -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 4.1 16.7 - - + +
353B ILE* 5.3 2.9 - - + -
355B VAL* 4.3 20.0 - - + -
376B LEU* 3.7 25.6 - - + -
377B GLN 3.3 9.2 - - - +
378B TYR* 3.6 22.2 - - + -
386B TRP* 4.3 0.4 - - - -
399B VAL* 5.5 2.2 - - + -
408B TYR* 5.7 2.2 - - + -
409B GLU* 1.3 75.8 - - - +
411B ARG* 1.3 70.9 + - - +
427B GLU 4.0 0.9 - - - +
428B VAL* 3.2 6.1 - - - -
429B LEU* 2.8 42.3 + - + +
431B VAL* 4.9 11.4 - - + -
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Residues in contact with ARG 411 (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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337B LEU* 5.3 0.2 - - - -
375B GLU 4.1 0.2 - - - +
376B LEU* 3.3 0.2 - - - -
377B GLN* 2.8 65.2 + - - +
386B TRP* 3.0 64.9 - - + +
410B VAL* 1.3 74.2 - - - +
412B VAL* 1.3 71.2 + - - +
425B PHE* 3.1 58.5 - - + +
426B SER* 4.0 11.2 - - - +
427B GLU 4.6 0.4 - - - -
428B VAL* 4.7 9.3 - - + +
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Residues in contact with VAL 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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334B PRO* 3.2 29.2 - - + +
337B LEU* 3.4 26.5 - - + -
357B TRP* 4.1 19.7 - - + -
374B TYR* 3.9 14.4 - - + -
375B GLU 3.3 12.1 - - - +
376B LEU* 4.0 16.8 - - + -
410B VAL* 4.2 0.9 - - + -
411B ARG* 1.3 83.5 - - - +
413B ARG* 1.3 69.9 + - - +
425B PHE* 3.6 3.1 - - - -
426B SER* 2.9 34.6 + - - +
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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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334B PRO* 4.3 1.3 - - - -
374B TYR* 3.2 11.8 - - - +
375B GLU* 2.8 59.9 + - + +
377B GLN* 3.5 8.1 - - - +
388B MET* 6.0 0.4 - - - -
412B VAL* 1.3 75.9 - - - +
414B SER* 1.3 59.8 + - - +
422B TYR* 3.6 40.2 - - + +
423B GLY 3.9 18.2 + - - +
424B GLU 4.5 3.6 - - - -
425B PHE* 3.5 39.0 - - + +
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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
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331B PRO* 3.1 11.5 - - - +
332B ASP 3.4 25.4 + - - -
334B PRO* 4.1 9.5 - - - +
360B PRO* 4.3 1.7 - - - +
372B LEU* 3.7 14.6 - - - +
373B GLU 3.7 2.2 - - - -
374B TYR* 3.4 24.3 - - - -
413B ARG* 1.3 78.2 - - - +
415B LYS* 1.3 60.3 + - - +
422B TYR* 3.0 3.3 - - - -
423B GLY 2.5 34.3 + - - +
424B GLU 4.6 2.6 + - - -
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Residues in contact with LYS 415 (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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25A PHE* 4.5 8.4 - - - -
29A GLN* 6.3 0.2 - - - +
331B PRO* 3.4 9.9 - - - -
372B LEU* 3.4 4.2 - - - +
373B GLU* 2.9 57.5 + - - +
414B SER* 1.3 73.0 - - - +
416B GLN* 1.3 66.8 + - - +
418B ASN 4.2 4.4 - - - +
419B SER* 3.0 45.6 + - - +
420B GLY 3.3 14.3 + - - -
421B ASN* 3.9 7.9 - - - +
422B TYR* 3.1 42.6 - - + +
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Residues in contact with GLN 416 (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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243B ARG* 3.0 50.2 + - - +
326B ASP* 3.5 9.7 + - - -
329B VAL* 4.0 18.9 - - + +
331B PRO* 3.9 6.5 - - - +
370B MET* 3.9 18.3 - - + +
371B VAL* 3.5 31.0 + - - +
372B LEU* 3.8 4.9 - - - -
415B LYS* 1.3 79.6 - - - +
417B ARG* 1.3 76.9 + - - +
418B ASN 3.0 3.8 + - - -
419B SER* 3.0 37.5 + - - +
421B ASN 4.6 0.4 + - - -
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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