Contacts of the strand formed by residues 377 - 383 (chain I) in PDB entry 1K9O
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 PRO 377 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I ASN* 3.3 30.8 + - - +
24I ASP* 3.8 18.8 - - - +
27I THR* 4.1 23.5 + - + +
48I PHE* 4.0 1.4 + - - +
265I LEU* 5.0 4.0 - - + -
370I GLU* 3.2 33.7 - - + +
371I LEU 3.2 10.3 - - - +
372I LYS* 3.4 16.1 - - - -
375I GLY 4.1 2.2 - - - +
376I ILE* 1.3 79.9 - - - +
378I MET* 1.3 63.7 + - - +
379I PHE 3.3 3.3 + - - +
380I ASN* 5.4 0.4 - - - +
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Residues in contact with MET 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I SER* 2.8 31.2 + - - -
47I ALA 5.0 0.2 - - - -
48I PHE* 3.2 45.2 - - + +
100I LEU* 3.9 14.6 - - + -
102I MET* 3.2 15.7 - - + -
371I LEU* 2.9 18.2 + - + +
373I ILE* 3.4 39.3 - - + -
376I ILE* 3.2 26.1 + - + +
377I PRO* 1.3 74.9 - - - +
379I PHE* 1.3 66.3 + - + +
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Residues in contact with PHE 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I THR* 6.1 0.7 - - - -
44I VAL* 4.7 13.0 - - + -
45I LEU 2.8 26.2 - - - +
46I SER* 3.7 4.3 - - - +
47I ALA 5.0 1.1 - - - +
100I LEU* 4.3 5.6 - - + -
178I ILE* 3.6 24.2 - - + -
180I PHE* 3.1 48.5 - + + -
241I MET* 6.2 1.3 - - - -
333I ILE* 4.5 13.0 - - + -
369I PHE* 4.9 3.4 - + - -
370I GLU* 3.2 7.2 - - - +
371I LEU* 3.0 67.1 + - + -
377I PRO 3.3 2.0 - - - -
378I MET* 1.3 85.1 - - + +
380I ASN* 1.3 68.8 + - - +
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Residues in contact with ASN 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I THR* 3.0 34.5 - - - +
31I PHE* 2.9 33.4 - - - -
44I VAL* 3.2 9.2 - - - +
45I LEU* 3.0 49.5 + - - +
47I ALA* 5.5 0.3 + - - +
368I TYR* 3.6 11.3 + - + +
369I PHE* 3.1 27.1 - - - +
370I GLU* 3.6 10.3 - - + +
377I PRO* 5.4 0.5 - - - +
379I PHE* 1.3 77.8 - - - +
381I GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I PHE* 3.8 13.9 - - - -
43I VAL* 3.3 18.8 - - - -
45I LEU* 4.6 0.7 - - - -
368I TYR* 3.0 24.1 - - - -
369I PHE* 3.2 17.8 + - - -
380I ASN* 1.3 82.8 - - - +
382I LYS* 1.3 62.0 + - - -
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Residues in contact with LYS 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I PHE* 4.7 4.7 - - + -
35I VAL* 3.9 25.5 - - + +
38I ASN 5.5 1.5 + - - -
39I PRO* 5.8 0.8 - - - +
40I GLY* 4.8 11.9 - - - +
41I GLN 3.3 22.0 - - - +
42I ASN* 3.4 5.7 - - - +
43I VAL* 3.3 34.7 + - + +
252I ILE* 4.5 15.1 - - + +
253I THR* 5.1 7.1 - - - +
256I GLU* 2.8 31.5 + - + +
367I PHE 3.1 15.3 - - - +
368I TYR* 4.5 2.0 - - - -
369I PHE* 3.3 3.7 - - - -
381I GLY* 1.3 76.1 - - - +
383I VAL* 1.3 67.0 + - - +
384I ILE* 3.6 18.8 - - - +
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Residues in contact with VAL 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I ASN* 3.3 10.8 - - - +
198I PHE* 4.1 1.4 - - - -
252I ILE* 6.5 0.2 - - - -
284I PHE* 3.6 22.7 - - + -
286I ILE* 3.7 4.9 - - + -
366I PRO* 3.1 5.4 - - - +
367I PHE* 2.7 61.9 + - + -
369I PHE* 3.5 21.3 - - + -
382I LYS* 1.3 77.0 - - - +
384I ILE* 1.3 61.8 + - - +
385I GLU 4.1 0.9 - - - +
386I PRO* 3.9 36.3 - - + -
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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