Contacts of the strand formed by residues 396 - 403 (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 SER 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B GLN* 2.6 31.8 + - - +
355B VAL 3.3 10.3 + - - -
356B ARG* 3.7 9.9 - - - +
357B TRP* 4.0 4.1 - - - -
392B ILE* 4.8 0.7 - - - +
394B THR* 3.2 22.5 + - - +
395B THR* 1.3 83.9 - - - +
397B VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 397 (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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354B GLN* 2.8 9.0 - - - +
355B VAL* 2.6 44.0 + - + +
357B TRP* 3.8 25.1 - - + -
376B LEU* 3.8 11.0 - - + -
389B MET* 3.6 28.5 - - + -
392B ILE* 5.0 18.8 - - + -
396B SER* 1.3 75.9 - - - +
398B PRO* 1.3 81.5 - - + +
399B VAL* 4.6 0.2 - - + -
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Residues in contact with PRO 398 (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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342B LEU* 4.1 14.1 - - + -
353B ILE 3.3 8.3 - - - +
354B GLN* 3.5 18.1 - - - +
389B MET* 3.4 17.7 - - - +
397B VAL* 1.3 100.4 - - + +
399B VAL* 1.3 59.8 + - - +
400B TYR* 3.9 35.7 + - + +
692C ILE* 5.9 1.3 - - + -
694C THR* 6.5 0.4 - - + -
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Residues in contact with VAL 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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351B ALA 4.3 1.4 - - - +
352B ASP* 3.5 2.9 - - - +
353B ILE* 2.6 45.6 + - + +
355B VAL* 3.9 29.4 - - + -
376B LEU* 4.5 6.3 - - + -
378B TYR* 4.1 32.1 - - + -
389B MET* 3.8 17.3 - - + -
397B VAL 4.2 2.9 - - - +
398B PRO* 1.3 78.6 - - - +
400B TYR* 1.3 63.5 + - - +
402B LEU* 4.0 24.7 - - + +
410B VAL* 5.5 2.2 - - + -
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Residues in contact with TYR 400 (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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342B LEU* 5.4 3.1 - - + -
352B ASP* 3.1 28.5 - - + -
378B TYR* 4.6 8.3 + - - -
398B PRO* 3.9 32.7 - - + +
399B VAL* 1.3 79.4 - - - +
401B SER* 1.3 73.6 + - - +
402B LEU* 3.4 11.0 + - - +
654C GLN* 5.7 3.6 - - - +
692C ILE* 3.3 30.0 - - + +
694C THR* 4.3 12.7 + - + +
696C SER 4.2 15.3 - - - -
697C VAL* 4.0 10.7 - - + +
698C PRO* 3.5 28.0 - - + -
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B HIS* 3.6 24.1 + - - -
351B ALA 3.6 1.1 - - - -
352B ASP* 3.3 3.8 + - - -
400B TYR* 1.3 82.3 - - - +
402B LEU* 1.3 65.5 + - - +
403B LYS* 3.7 6.4 + - - +
408B TYR* 5.0 0.7 + - - -
642C LEU* 4.5 10.7 - - - +
654C GLN* 4.1 9.9 + - - -
698C PRO* 3.8 10.7 - - - +
700C TYR* 3.1 25.7 + - - -
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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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350B HIS* 3.1 6.5 - - - -
351B ALA 2.6 41.8 + - - +
353B ILE* 3.8 41.5 - - + -
378B TYR* 3.8 31.4 - - + -
399B VAL* 4.0 17.3 - - + +
400B TYR 4.0 7.0 - - - +
401B SER* 1.3 74.6 - - - +
403B LYS* 1.3 61.2 + - - +
404B VAL 3.7 0.2 - - - -
408B TYR* 3.9 36.6 - - + -
431B VAL* 4.8 2.0 - - + -
433B LEU* 4.3 12.6 - - + -
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Residues in contact with LYS 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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349B ILE* 3.4 17.5 - - + +
350B HIS* 3.5 22.1 - - + +
401B SER 4.6 5.4 - - - +
402B LEU* 1.3 69.7 - - - +
404B VAL* 1.3 57.0 + - - +
405B ASP* 3.0 13.2 - - - +
406B LYS* 2.8 53.8 + - + +
408B TYR* 3.4 18.6 + - - +
433B LEU* 3.9 2.1 - - - +
643C ASN* 3.5 27.7 - - - +
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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