Contacts of the strand formed by residues 374 - 380 (chain D) in PDB entry 1K9I
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 PHE 374 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271D SER* 3.5 23.3 - - - +
272D ASN 3.1 24.9 - - - -
273D SER 3.4 11.2 - - - -
274D GLN* 3.7 33.4 - - + -
312D ARG* 3.3 60.6 - - + -
313D PHE 3.3 10.6 + - - +
314D THR* 3.1 13.2 - - + +
315D TRP* 2.7 24.1 + - - +
373D LYS* 1.3 79.2 - - - +
375D TRP* 1.3 60.9 + - - +
310I SER* 6.4 0.2 - - - -
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Residues in contact with TRP 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D PHE* 4.9 2.6 - - - -
271D SER* 3.0 50.7 + - - -
273D SER* 2.8 44.0 - - - -
275D ARG* 3.3 37.7 - - + -
280D SER* 3.4 34.4 + - - +
283D ALA* 4.1 13.5 - - + +
284D CYS* 3.8 20.7 - - - -
291D LEU* 3.9 10.3 - - + -
314D THR* 3.4 6.4 - - - +
315D TRP* 3.8 6.3 - - + -
373D LYS 3.4 10.1 - - - -
374D PHE* 1.3 75.8 - - - +
376D ILE* 1.3 69.2 + - - +
377D CYS* 3.5 18.9 - - - -
258I TRP* 5.0 1.7 - + - -
259I GLU* 3.4 18.4 - - + -
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Residues in contact with ILE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D TYR* 4.3 6.5 - - + -
269D PHE 3.0 10.8 - - - +
270D MET* 3.9 35.7 - - + -
291D LEU* 3.6 6.2 - - - +
292D VAL* 2.8 41.7 + - + +
303D LEU* 4.2 30.1 - - + +
306D GLN* 5.3 2.2 - - + -
307D SER* 4.0 17.7 - - - +
314D THR* 3.5 20.0 - - + -
315D TRP 3.7 5.8 + - - +
359D PHE* 4.2 8.1 - - + -
375D TRP* 1.3 85.0 - - - +
377D CYS* 1.3 65.5 + - - +
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Residues in contact with CYS 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D TRP* 4.0 12.3 - - + -
268D TYR* 3.2 6.1 - - - -
269D PHE* 2.9 34.6 + - + -
284D CYS* 2.1 53.8 - - - -
289D ALA* 3.8 14.4 - - + -
290D GLN 3.6 1.1 - - - -
375D TRP* 3.5 16.4 - - - -
376D ILE* 1.3 76.2 - - - +
378D LYS* 1.3 60.7 + - - +
258I TRP* 4.1 15.9 - - - -
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Residues in contact with LYS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D TRP* 4.9 0.2 - - - -
266D ASN* 3.5 25.9 - - + +
267D CYS 3.3 7.2 - - - +
268D TYR* 3.5 26.0 - - + -
289D ALA* 3.4 2.3 - - - +
290D GLN* 2.9 38.4 + - + +
292D VAL* 4.2 9.9 - - + -
293D VAL* 3.1 25.0 + - + +
295D LYS* 4.1 14.1 - - - +
299D GLU* 2.6 35.9 + - - +
377D CYS* 1.3 76.4 - - - +
379D LYS* 1.3 70.8 + - - +
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Residues in contact with LYS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PRO* 4.0 28.2 - - - +
260D TRP* 4.0 28.9 - - + -
266D ASN* 3.4 6.9 - - - -
267D CYS* 2.6 39.8 + - + -
287D VAL* 3.2 23.0 + - - +
288D GLY 3.8 23.3 - - - +
289D ALA* 4.1 7.9 - - + -
378D LYS* 1.3 81.2 - - - +
380D SER* 1.3 64.3 + - - +
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Residues in contact with SER 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D GLY 3.8 3.8 - - - -
266D ASN* 3.2 18.4 + - - -
267D CYS* 4.2 2.1 - - - -
379D LYS* 1.3 88.2 - - - +
381D ALA* 1.3 69.8 + - - +
382D ALA 4.0 0.2 + - - -
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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