Contacts of the strand formed by residues 402 - 410 (chain B) in PDB entry 1KP5
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 TYR 402 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B GYS 4.3 0.5 + - - -
378B VAL* 4.1 2.4 - - - -
379B GLN 3.8 8.8 + - - -
380B CYS* 3.7 26.8 + - + +
393B PHE* 4.1 15.7 - + + -
394B PHE* 3.6 42.6 - + + -
397B ALA* 4.0 10.8 - - + -
398B MET* 4.8 2.7 - - - -
401B GLY* 1.3 76.6 - - - +
403B VAL* 1.3 65.4 + - - +
404B GLN* 3.8 7.8 + - + -
421B GLU* 3.5 3.1 - - - -
422B VAL* 2.9 65.2 + - + +
495B ASN* 3.2 26.9 - - - -
496B THR 3.3 18.8 - - - +
498B ILE* 3.7 8.7 - - - +
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Residues in contact with VAL 403 (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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402B TYR* 1.3 73.6 - - - +
404B GLN* 1.3 61.8 + - - +
405B GLU* 3.8 24.0 - - + +
419B ARG* 3.8 20.2 - - + +
420B ALA 3.3 8.5 - - - +
421B GLU* 4.2 7.4 - - + -
494B GLN 3.7 0.7 - - - +
495B ASN* 3.1 7.6 - - - +
496B THR* 2.8 44.5 + - - +
497B PRO 5.3 1.1 - - - +
498B ILE* 3.8 22.9 - - + -
923B SO4 3.3 26.7 - - - +
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Residues in contact with GLN 404 (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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373B THR* 5.3 1.8 + - - +
376B GYS 3.0 38.3 + - - +
379B GLN* 3.6 6.2 - - - +
402B TYR* 3.8 14.7 + - + -
403B VAL* 1.3 74.5 - - - +
405B GLU* 1.3 64.7 + - - +
406B ARG* 3.3 23.0 - - + +
418B THR* 4.0 3.1 + - - +
419B ARG* 3.6 1.6 + - - -
420B ALA* 2.7 46.2 + - + +
422B VAL* 5.1 2.7 - - + -
493B GLN* 3.3 20.2 + - + +
494B GLN 3.7 2.2 - - - -
495B ASN* 2.8 32.9 + - - +
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Residues in contact with GLU 405 (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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403B VAL* 3.8 19.2 - - + +
404B GLN* 1.3 76.9 - - - +
406B ARG* 1.3 69.2 + - - +
418B THR* 3.2 11.2 - - - +
419B ARG* 4.2 17.1 - - + +
492B TYR 3.7 0.2 - - - +
493B GLN* 3.4 1.2 - - - +
494B GLN* 3.1 57.3 + - + +
496B THR* 5.3 3.1 + - - +
923B SO4 3.4 26.4 + - - -
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Residues in contact with ARG 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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372B THR* 2.9 31.1 + - - -
373B THR* 4.1 6.7 + - - +
376B GYS 2.9 36.8 + - - +
379B GLN* 4.1 0.6 + - - -
404B GLN* 3.3 18.4 - - + +
405B GLU* 1.3 81.7 - - - +
407B THR* 1.3 64.8 + - - +
408B ILE* 4.1 10.3 - - + -
417B LYS* 3.4 4.7 - - - +
418B THR* 2.9 44.6 + - - +
475B PHE* 3.8 13.3 - - - -
491B HIS* 3.6 23.6 - - - -
492B TYR 3.1 11.9 - - - +
493B GLN* 2.7 40.8 + - + +
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Residues in contact with THR 407 (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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406B ARG* 1.3 77.4 + - - +
408B ILE* 1.3 67.1 + - - +
409B SER* 4.8 5.4 - - - +
415B ASN* 4.8 6.1 - - + +
416B TYR 3.4 7.2 - - - +
417B LYS* 4.1 32.1 - - - +
490B ASP 3.3 3.8 - - - +
491B HIS* 3.6 1.0 - - - -
492B TYR* 3.1 47.0 + - + +
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Residues in contact with ILE 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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369B THR 4.9 3.4 - - - +
372B THR* 3.9 8.3 - - - +
373B THR* 4.0 16.4 - - - +
406B ARG* 4.4 15.0 - - + -
407B THR* 1.3 76.5 - - - +
409B SER* 1.3 61.2 + - - +
410B PHE* 3.7 27.6 + - + -
415B ASN* 3.1 6.1 - - - -
416B TYR* 2.8 58.6 + - + -
418B THR* 5.3 2.5 - - + -
489B ALA* 4.0 7.6 - - + -
490B ASP 3.2 4.5 - - - +
491B HIS* 3.3 48.9 - - + +
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Residues in contact with SER 409 (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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407B THR* 3.9 6.7 - - - -
408B ILE* 1.3 72.5 - - - +
410B PHE* 1.3 64.8 + - - +
411B LYS* 3.6 2.9 + - - -
413B ASP 5.4 0.9 + - - -
414B GLY 5.0 0.3 + - - -
415B ASN* 4.0 12.1 - - - +
489B ALA* 3.6 0.6 - - - -
490B ASP* 2.8 51.0 + - - +
492B TYR* 5.1 7.6 - - - -
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Residues in contact with PHE 410 (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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369B THR* 3.8 29.6 - - + -
408B ILE* 3.7 19.5 - - + -
409B SER* 1.3 73.9 + - - +
411B LYS* 1.3 67.4 + - - +
412B ASP 3.3 0.5 + - - -
413B ASP* 3.0 30.2 + - + +
414B GLY 3.2 20.1 + - - +
416B TYR* 3.5 48.9 - + - -
440B PHE* 3.6 11.7 - + - -
446B ILE* 4.0 17.0 - - + -
479B HIS* 4.2 7.0 - + - -
487B GLN* 3.9 12.8 - - + +
488B LEU 3.4 9.0 - - - -
489B ALA* 3.7 21.3 - - + -
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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