Contacts of the strand formed by residues 398 - 409 (chain B) in PDB entry 3KCZ
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 THR 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLN* 5.5 3.6 - - - -
390B HIS* 3.9 8.3 - - + +
395B SER 6.1 0.2 - - - +
397B TYR* 1.3 81.8 - - - +
399B MET* 1.3 63.4 + - - +
577B PHE* 3.5 2.9 - - - -
578B ASN* 2.6 57.0 + - - +
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Residues in contact with MET 399 (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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386B LEU* 3.7 29.4 - - + +
387B GLN* 2.8 31.2 + - - +
390B HIS* 3.6 24.1 + - + +
397B TYR* 3.8 13.9 - - + -
398B THR* 1.3 81.6 - - - +
400B THR* 1.3 62.3 + - - +
467B SER* 3.6 25.4 - - - +
468B SER* 4.1 3.4 - - - -
471B ALA* 3.6 31.9 - - + -
485B LEU* 4.2 3.8 - - - -
575B VAL* 3.7 23.1 - - + -
576B GLN 3.3 3.1 - - - -
577B PHE* 4.2 6.3 - - + -
578B ASN* 3.9 0.4 + - - -
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 4.9 0.4 - - - -
387B GLN* 4.7 0.9 - - - +
399B MET* 1.3 71.8 + - - +
401B LEU* 1.3 70.8 + - - +
402B LEU* 3.4 11.2 + - + -
575B VAL* 3.5 4.4 - - - -
576B GLN* 2.7 56.7 + - - +
578B ASN* 2.8 26.0 + - - -
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Residues in contact with LEU 401 (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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374B HIS* 4.7 2.1 - - - -
379B PHE* 3.7 33.9 - - + +
382B ILE* 4.5 5.6 - - + -
383B SER* 3.5 37.0 - - - +
386B LEU* 4.0 13.7 - - + +
387B GLN* 5.1 1.8 - - - +
399B MET 4.2 0.4 - - - -
400B THR* 1.3 76.9 - - - +
402B LEU* 1.3 60.9 + - - +
403B ASP 3.3 25.6 - - - +
404B LEU* 4.8 3.4 - - + -
573B LEU* 3.5 40.8 - - + -
574B LYS 3.7 5.8 - - - +
575B VAL* 4.4 3.4 - - + +
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Residues in contact with LEU 402 (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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374B HIS* 3.1 21.7 + - - -
400B THR* 4.3 9.9 - - + +
401B LEU* 1.3 75.0 - - - +
403B ASP* 1.3 66.0 + - + +
482B THR* 4.7 9.0 - - + +
574B LYS* 2.8 42.8 + - + +
575B VAL 4.4 2.0 - - - +
576B GLN* 3.6 49.1 - - + +
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Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ARG* 3.0 51.7 + - - +
374B HIS* 2.9 22.0 + - - -
379B PHE* 4.7 0.7 - - - -
401B LEU* 3.3 13.6 - - - +
402B LEU* 1.3 82.3 - - - +
404B LEU* 1.3 65.4 + - - +
405B PHE* 4.0 20.4 - - + -
573B LEU* 3.7 0.2 - - - -
574B LYS* 3.0 35.8 + - + +
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Residues in contact with LEU 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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371B PRO* 3.5 5.0 - - - +
372B LEU* 3.0 50.5 + - + +
379B PHE* 3.7 49.1 - - + +
382B ILE* 3.9 29.8 - - + -
401B LEU* 4.8 2.2 - - + -
403B ASP* 1.3 81.1 + - - +
405B PHE* 1.3 64.7 + - - +
571B TYR* 4.2 6.3 - - + -
572B LEU 3.6 7.9 - - - +
573B LEU* 3.7 36.6 - - + -
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Residues in contact with PHE 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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237B ARG* 3.7 37.7 - - + -
238B VAL* 4.0 13.9 - - + -
241B LEU* 3.8 35.2 - - + -
369B LEU* 4.5 8.3 - - + -
370B ARG 3.3 12.3 - - - +
371B PRO* 3.8 22.4 - - + -
372B LEU* 4.6 2.5 - - - -
403B ASP* 4.0 30.7 - - + -
404B LEU* 1.3 75.6 - - - +
406B GLU* 1.3 62.4 + - - +
407B VAL* 4.6 0.2 - - - -
484B LEU* 6.4 0.2 - - + -
571B TYR* 3.2 9.1 - - - +
572B LEU* 2.8 53.0 + - + +
574B LYS* 4.6 11.0 - - + -
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Residues in contact with GLU 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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368B ALA 3.6 1.2 - - - +
369B LEU* 3.3 6.9 + - - -
370B ARG* 2.7 69.3 + - + +
372B LEU* 4.0 22.8 - - + +
405B PHE* 1.3 73.2 - - - +
407B VAL* 1.3 66.3 + - - +
408B GLU* 4.9 1.1 - - + +
570B ARG* 3.3 39.4 + - - +
571B TYR* 4.3 7.8 - - + -
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Residues in contact with VAL 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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367B CYS* 3.5 25.8 - - - -
368B ALA 3.5 3.1 - - - +
369B LEU* 3.9 10.8 - - + -
405B PHE 4.0 0.2 - - - +
406B GLU* 1.3 78.1 - - - +
408B GLU* 1.3 61.7 + - - +
409B LYS 4.0 3.1 - - - +
439B LEU* 4.4 5.4 - - + -
486B LEU* 4.5 4.9 - - + -
569B MET* 3.3 33.9 - - + +
570B ARG* 2.8 39.5 + - - +
571B TYR 3.7 5.8 - - - +
572B LEU* 3.6 37.2 - - + +
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Residues in contact with GLU 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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367B CYS* 3.6 0.8 - - - -
368B ALA* 3.0 37.3 + - + +
370B ARG* 2.8 42.5 + - - +
406B GLU* 4.1 2.1 + - + +
407B VAL* 1.3 73.4 - - - +
409B LYS* 1.3 64.2 + - - +
410B ASP* 3.6 6.5 + - - +
413B LYS* 4.8 17.5 - - + +
568B ARG* 4.8 7.5 + - - +
569B MET 5.0 0.9 - - - -
570B ARG* 4.6 12.2 + - - +
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Residues in contact with LYS 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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365B LEU 2.8 21.2 + - - -
366B HIS* 2.9 24.3 + - - +
367B CYS* 3.8 8.8 - - + -
407B VAL* 4.0 2.8 - - + +
408B GLU* 1.3 76.9 - - - +
410B ASP* 1.3 79.4 + - - +
411B GLY 3.2 2.6 + - - -
412B GLU* 3.2 36.5 + - + +
413B LYS* 4.6 2.1 + - - +
439B LEU 3.2 15.9 - - - +
440B SER 2.6 30.9 + - - -
441B HIS* 4.5 2.5 - - - +
442B GLY* 4.7 5.2 - - - +
569B MET* 3.7 27.4 + - + -
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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