Contacts of the helix formed by residues 313 - 333 (chain C) in PDB entry 3HYW
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 313 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C PRO* 4.3 19.5 - - + -
312C LYS* 1.3 73.9 - - - +
314C GLY* 1.3 59.3 + - - +
315C MET* 3.7 2.8 + - - +
316C MET* 3.2 25.5 + - - +
317C ILE* 2.9 30.3 + - - +
345C ALA* 3.3 23.1 - - + +
347C CSS 3.7 23.2 - - - -
363C VAL* 5.5 1.6 - - + -
441C FAD 3.5 18.6 - - - -
800C PS9 4.9 10.1 - - - -
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.6 8.7 - - - +
313C THR* 1.3 71.2 - - - +
315C MET* 1.3 55.0 + - - +
317C ILE* 3.2 7.6 + - - +
318C GLU* 2.8 34.3 + - - +
441C FAD 2.7 35.1 + - - -
500C DCQ 3.4 15.7 - - - -
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Residues in contact with MET 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C THR* 3.3 2.9 + - - +
314C GLY* 1.3 72.1 - - - +
316C MET* 1.3 66.4 + - - +
318C GLU* 3.3 5.8 + - + +
319C GLN* 3.0 41.0 + - + +
344C SER* 3.4 34.5 - - - +
345C ALA* 3.9 7.6 - - - -
346C ILE* 3.3 45.3 - - + +
359C PHE* 4.5 1.1 - - + -
407C LEU* 4.1 11.2 - - + -
413C VAL* 3.6 28.0 - - + -
500C DCQ 2.9 34.9 + - + +
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Residues in contact with MET 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ILE* 5.1 5.2 - - + -
310C VAL* 4.8 6.1 - - + -
311C PRO 3.4 21.5 - - - +
312C LYS* 4.3 5.8 - - + -
313C THR* 3.2 39.3 + - - +
315C MET* 1.3 76.6 - - - +
317C ILE* 1.3 58.0 + - - +
319C GLN* 3.3 9.1 + - - +
320C MET* 3.0 41.1 + - + +
343C LEU* 3.6 31.7 - - + +
344C SER 3.5 17.2 + - - +
363C VAL* 3.8 32.8 - - + -
364C ILE* 5.4 4.9 - - + -
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.2 7.6 - - + +
13C GLY* 3.5 34.8 - - - +
292C VAL* 4.0 1.8 - - + -
293C GLY* 3.7 27.8 - - - -
294C VAL 4.2 2.5 - - - +
312C LYS* 3.4 29.4 - - + +
313C THR 2.9 18.8 + - - +
314C GLY* 3.6 4.9 - - - +
316C MET* 1.3 74.3 - - - +
318C GLU* 1.3 58.1 + - - +
320C MET* 3.3 8.4 + - - +
321C ALA* 2.9 27.9 + - - +
441C FAD 3.5 32.8 - - - +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.7 7.8 - - + +
16C ALA* 4.9 3.6 - - + -
20C ASN* 4.6 0.7 + - - -
314C GLY* 2.8 19.1 + - - +
315C MET* 3.6 5.6 - - + +
317C ILE* 1.3 73.1 - - - +
319C GLN* 1.3 57.9 + - + +
321C ALA* 3.5 7.5 + - - +
322C MET* 3.0 43.6 + - + +
385C PHE* 4.1 0.9 - - - -
389C PHE* 3.6 28.0 - - + -
392C LYS* 3.6 18.1 + - - -
398C ILE* 3.9 19.1 - - + +
403C GLU* 3.6 9.9 - - - +
500C DCQ 2.7 35.2 + - + +
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Residues in contact with GLN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C MET* 3.0 41.4 + - + +
316C MET 3.6 4.3 - - - +
318C GLU* 1.3 75.9 - - + +
320C MET* 1.3 64.5 + - - +
322C MET* 3.3 12.6 + - + +
323C ALA 3.0 18.9 + - - -
341C PRO* 3.5 10.6 - - + +
342C ARG* 4.3 0.6 - - - +
343C LEU* 2.7 33.5 + - - -
344C SER* 2.9 31.8 + - - +
413C VAL* 4.0 2.4 - - - +
415C PRO* 3.6 44.1 - - + +
416C ILE* 3.5 7.1 - - - +
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Residues in contact with MET 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 3.6 45.3 - - + -
292C VAL* 4.1 8.7 - - + -
293C GLY* 3.3 29.6 - - - +
296C THR* 4.3 0.4 - - - +
298C ILE* 4.1 4.5 - - + -
312C LYS* 3.9 32.3 - - + -
316C MET* 3.0 26.7 + - + +
317C ILE* 3.4 9.6 - - - +
319C GLN* 1.3 73.3 - - - +
321C ALA* 1.3 55.2 + - - +
323C ALA* 3.2 2.8 + - - +
324C VAL* 2.8 40.1 + - - +
341C PRO* 3.7 9.6 - - - +
343C LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 4.2 2.5 - - - +
16C ALA* 3.6 27.8 - - + -
17C THR* 3.3 30.4 - - - +
20C ASN* 3.5 5.3 + - - +
292C VAL* 4.0 4.9 - - + +
317C ILE 2.9 17.4 + - - +
318C GLU 3.6 4.5 - - - +
319C GLN 3.3 0.2 - - - -
320C MET* 1.3 74.9 - - - +
322C MET* 1.3 57.4 + - - +
324C VAL* 4.1 0.2 - - - -
325C ALA* 3.0 31.7 + - - +
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Residues in contact with MET 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASN* 3.4 20.6 - - - +
318C GLU* 3.0 38.0 + - + +
319C GLN* 3.5 13.2 - - + +
321C ALA* 1.3 73.2 - - - +
323C ALA* 1.3 64.8 + - - +
325C ALA* 3.8 1.1 - - - +
326C HIS* 3.1 36.2 + - + -
399C ALA* 4.6 18.4 - - + -
404C GLU* 4.6 8.1 - - + +
415C PRO* 3.6 40.6 - - + -
416C ILE* 3.8 12.8 - - + -
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Residues in contact with ALA 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C CYS 5.2 1.3 - - - +
281C PHE* 5.9 0.2 - - + -
319C GLN 3.0 17.4 + - - +
320C MET 3.6 3.6 - - - +
322C MET* 1.3 72.7 - - - +
324C VAL* 1.3 61.2 + - + +
326C HIS* 3.3 3.6 + - - +
327C ASN* 2.8 36.6 + - - +
339C TYR* 3.6 27.1 - - - +
341C PRO* 3.8 23.3 - - + -
416C ILE* 3.7 10.4 - - + +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.9 14.1 - - + -
102C VAL* 4.0 3.6 - - + -
280C CYS 4.2 1.3 - - - +
281C PHE* 3.8 28.7 - - + +
290C PHE* 3.5 36.6 - - + -
292C VAL* 3.7 20.4 - - + -
320C MET 2.8 23.7 + - - +
321C ALA 4.1 1.8 - - - +
323C ALA* 1.3 72.3 - - + +
325C ALA* 1.3 58.5 + - - +
327C ASN* 3.0 8.3 + - - +
328C ILE* 2.9 41.9 + - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 4.3 2.7 - - + +
20C ASN* 3.5 25.6 - - + -
21C LEU* 3.7 27.9 - - + +
24C LEU* 4.0 8.7 - - + -
321C ALA 3.0 19.7 + - - +
322C MET 3.8 3.1 - - - +
324C VAL* 1.3 77.6 - - - +
326C HIS* 1.3 61.9 + - + +
328C ILE 3.4 0.2 + - - -
329C VAL* 3.0 28.9 + - - +
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Residues in contact with HIS 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 3.9 34.8 - - + +
322C MET* 3.1 30.4 + - + +
323C ALA 3.7 3.8 - - - +
325C ALA* 1.3 78.8 - - + +
327C ASN* 1.3 58.2 + - - +
329C VAL* 4.6 2.6 - - - +
330C ASN* 2.9 41.0 + - - +
339C TYR* 3.7 27.1 + + + -
416C ILE* 3.8 22.0 - - + +
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Residues in contact with ASN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C CYS* 3.1 23.0 - - - +
290C PHE* 3.7 21.2 - - + -
323C ALA 2.8 22.4 + - - +
324C VAL 3.0 5.1 + - - +
326C HIS* 1.3 77.6 - - - +
328C ILE* 1.3 60.5 + - - +
331C ASP* 3.2 23.4 + - - +
338C LYS* 3.3 31.0 - - + +
339C TYR* 2.7 51.9 - - - +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C VAL* 4.4 5.6 - - + -
21C LEU* 3.9 27.8 - - + -
28C LEU* 5.4 0.2 - - + -
100C TYR* 3.6 37.6 + - + -
102C VAL* 3.6 29.8 - - + -
290C PHE* 3.5 27.1 - - + -
324C VAL* 2.9 26.3 + - + +
327C ASN* 1.3 72.5 - - - +
329C VAL* 1.3 59.8 + - - +
331C ASP* 3.2 7.9 + - - +
332C ILE* 2.9 37.9 + - + +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 4.1 13.7 - - + +
24C LEU* 3.9 35.4 - - + +
25C MET* 3.5 36.1 - - + -
28C LEU* 5.0 0.9 - - + -
325C ALA 3.0 21.0 + - - +
326C HIS* 4.0 5.2 - - - +
328C ILE* 1.3 74.3 - - - +
330C ASN* 1.3 65.0 + - - +
332C ILE* 3.3 5.3 + - - +
333C ARG* 3.0 44.7 + - - +
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Residues in contact with ASN 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C HIS* 2.9 25.2 + - - +
327C ASN 4.1 2.0 - - - +
329C VAL* 1.3 83.8 - - - +
331C ASP* 1.3 57.2 - - - +
333C ARG* 3.4 3.6 + - - +
334C ASN 3.0 6.6 + - - -
335C ASN* 2.6 68.7 + - + +
337C ASP* 2.8 31.4 + - - +
338C LYS* 4.0 2.2 - - - +
339C TYR* 3.7 21.6 + - - -
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Residues in contact with ASP 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C TYR* 2.6 34.1 + - + +
282C GLN* 5.8 2.9 + - - -
287C LYS 6.0 1.6 - - - -
290C PHE* 5.9 2.0 - - + -
327C ASN 3.2 19.0 + - - +
328C ILE* 3.5 5.2 - - - +
330C ASN* 1.3 72.5 - - - +
332C ILE* 1.3 65.1 + - - +
334C ASN* 3.2 19.5 + - - +
335C ASN 4.7 0.2 - - - -
338C LYS* 4.1 15.3 + - - +
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Residues in contact with ILE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 4.0 20.6 - - + +
25C MET* 3.9 26.2 - - + -
28C LEU* 3.6 32.3 - - + -
100C TYR* 3.5 31.2 + - + +
328C ILE* 2.9 28.0 + - + +
329C VAL* 3.4 7.6 - - - +
331C ASP* 1.3 78.7 - - - +
333C ARG* 1.3 60.8 + - + +
334C ASN* 3.5 5.5 + - - -
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Residues in contact with ARG 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU 5.4 4.8 + - - -
25C MET* 3.6 28.0 - - + +
329C VAL* 3.0 26.7 + - - +
330C ASN* 4.2 5.8 + - - +
331C ASP 3.2 0.4 - - - -
332C ILE* 1.3 78.1 - - + +
334C ASN* 1.3 70.8 + - - +
335C ASN* 3.2 6.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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