Contacts of the helix formed by residues 338 - 349 (chain K) in PDB entry 5GJQ
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 ARG 338 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337K ASP* 1.3 85.5 - - + +
339K ARG* 1.3 70.7 + - - +
341K LYS* 3.0 7.6 + - - +
342K ARG* 3.0 29.4 + - - +
364K VAL* 3.4 30.9 - - + +
365K ALA* 3.6 35.1 + - - +
366K ARG 4.9 2.0 - - - +
199i GLU* 5.4 8.3 - - + +
200i GLY* 3.3 43.4 + - - +
201i GLN* 3.7 10.1 - - - +
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Residues in contact with ARG 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K ASP* 4.8 11.7 + - - -
172K ILE* 6.4 0.6 - - - +
337K ASP* 3.6 9.3 + - - +
338K ARG* 1.3 75.5 - - - +
340K GLN* 1.3 81.1 + - - +
342K ARG* 2.6 42.0 + - + +
343K LEU* 3.2 28.5 + - + +
201Q TYR* 2.4 49.5 + - - +
203Q PRO* 6.2 1.1 - - - -
204Q PRO* 6.3 2.9 - - - -
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Residues in contact with GLN 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K GLY 4.2 15.8 + - - +
170K MET* 4.2 23.3 - - - +
173K GLN* 4.3 5.9 + - - -
334K PRO* 4.2 17.0 - - - +
336K PRO* 3.0 31.6 - - + +
337K ASP* 3.2 18.7 + - - +
338K ARG 3.4 0.2 - - - -
339K ARG* 1.3 90.2 - - - +
341K LYS* 1.3 52.9 + - - +
343K LEU* 2.8 17.7 + - + +
344K ILE* 2.8 46.9 + - + +
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Residues in contact with LYS 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336K PRO* 3.9 11.7 - - + -
337K ASP* 2.4 40.4 + - - +
338K ARG* 3.0 12.2 + - - +
340K GLN* 1.3 77.8 - - - +
342K ARG* 1.3 51.8 + - - +
344K ILE* 2.9 10.7 + - + -
345K PHE* 2.4 44.4 + - + +
363K TYR 5.7 1.6 - - - +
364K VAL* 4.6 20.4 - - + +
366K ARG 4.4 4.0 + - - +
367K PRO* 2.5 31.7 + - - +
368K ASP* 4.8 1.4 - - - +
369K LYS* 3.3 12.5 - - - +
370K ILE* 3.6 25.2 - - + +
375K ILE* 5.2 10.1 - - + -
403K TYR* 5.8 2.5 - - - +
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Residues in contact with ARG 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338K ARG* 3.0 21.1 + - - +
339K ARG* 2.6 37.4 + - + +
341K LYS* 1.3 71.3 - - - +
343K LEU* 1.3 51.9 + - + +
345K PHE* 3.9 1.5 - - - +
346K SER* 2.6 40.8 + - - -
361K GLU* 4.1 23.0 + - - +
364K VAL* 3.4 37.8 - - + +
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Residues in contact with LEU 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY 4.4 1.3 - - - -
169K GLY* 3.1 40.4 - - - +
171K ASP* 5.4 1.8 - - - +
339K ARG* 3.9 36.3 - - + +
340K GLN* 2.8 10.8 + - + +
342K ARG* 1.3 80.6 - - + +
344K ILE* 1.3 53.6 + - - +
346K SER* 3.3 6.3 - - - +
347K THR* 2.3 49.0 + - + +
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Residues in contact with ILE 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY 4.7 1.3 - - - +
169K GLY 5.5 1.3 - - - +
336K PRO* 3.5 31.6 - - + -
340K GLN* 2.8 33.6 + - + +
341K LYS* 3.4 10.8 - - - +
343K LEU* 1.3 72.2 - - + +
345K PHE* 1.3 60.7 + - - +
347K THR* 2.5 21.6 + - - +
348K ILE* 2.8 41.7 + - + +
372K GLY* 3.8 23.8 - - - +
375K ILE* 3.9 11.4 - - + -
501K ADP 3.9 30.3 - - + +
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Residues in contact with PHE 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341K LYS* 2.4 32.6 + - + +
342K ARG* 3.9 4.7 - - - +
344K ILE* 1.3 66.1 - - - +
346K SER* 1.3 54.5 + - - +
348K ILE* 3.0 6.0 + - + +
349K THR* 2.7 42.2 + - - +
360K LEU* 2.3 64.2 - - + -
363K TYR* 3.5 15.0 - - + -
364K VAL* 3.8 11.2 - - + -
375K ILE* 2.9 41.1 - - + -
378K ILE* 4.5 15.5 - - + -
379K CYS* 4.7 4.9 - - - -
399K PHE* 6.2 0.2 - + - -
403K TYR* 3.9 22.2 - + - -
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Residues in contact with SER 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342K ARG 2.6 27.8 + - - -
343K LEU* 2.9 22.3 + - - +
345K PHE* 1.3 72.2 - - - +
347K THR* 1.3 60.2 + - - +
349K THR* 3.5 7.5 + - - -
350K SER* 2.8 31.1 + - - -
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Residues in contact with THR 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K ALA 5.1 4.3 - - - +
166K ASP* 4.2 21.4 + - - +
168K GLY* 4.4 19.7 - - - -
343K LEU* 2.3 34.2 + - + +
344K ILE* 2.5 27.5 + - - +
346K SER* 1.3 80.6 - - - +
348K ILE* 1.3 62.9 + - - +
350K SER* 2.5 24.8 + - - -
351K LYS* 3.8 8.8 + - - +
501K ADP 4.7 4.3 + - - -
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Residues in contact with ILE 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K ASP* 6.0 1.3 - - - +
344K ILE* 2.8 37.2 + - + +
345K PHE* 3.6 2.2 - - + +
347K THR* 1.3 78.5 + - - +
349K THR* 1.3 58.7 + - - +
350K SER 3.1 2.2 + - - -
351K LYS* 3.5 17.6 + - - +
352K MET* 3.9 8.0 - - - +
372K GLY 4.7 1.1 - - - +
375K ILE* 3.3 42.8 - - + +
376K ASN* 3.8 17.0 - - + +
379K CYS* 2.0 54.7 - - + -
501K ADP 5.8 6.1 - - + +
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Residues in contact with THR 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345K PHE 2.7 30.6 + - - +
346K SER* 3.5 9.1 + - - -
348K ILE* 1.3 69.2 - - - +
350K SER* 1.3 60.1 - - - +
351K LYS 3.3 2.0 + - - -
352K MET* 4.0 20.3 + - - +
353K ASN 4.0 12.6 - - - +
354K LEU* 4.2 25.2 - - + +
360K LEU* 3.8 25.8 - - + +
379K CYS* 4.0 13.0 - - - -
399K PHE* 4.4 8.3 - - + -
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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